poy4 - Project Hosting on Google Code

Earlier this year Oct 15, 2009 Repository synced up to r193 by avaron Aug 06, 2009 Repository synced up to r191 by avaron Aug 05, 2009 Repository synced up to r189 by avaron Aug 05, 2009 Repository synced up to r187 by avaron Aug 05, 2009 Repository synced up to r185 by avaron Aug 03, 2009 Repository synced up to r183 by avaron Jul 10, 2009 Repository synced up to r181 by avaron Jul 08, 2009 Repository synced up to r179 by avaron Jun 19, 2009 issue 76 (error during wagner builds for annotated data ) reported by me...@amnh.org - What steps will reproduce the problem? 1. read (annotated:("deca_dup_tridaph")) 2. transform (dynamic_pam:(locus_inversion:20, locus_indel:(9,0))) 3. build () What is the expected output? What do you see instead? At the end of the 4th wagner build this error appears.... Error : File "sequence.ml", line 705, characters 8-14: Assertion failed Fatal error: exception Assert_failure("sequence.ml", 705, 8) Please use labels and text to provide additional information. What steps will reproduce the problem? 1. read (annotated:("deca_dup_tridaph")) 2. transform (dynamic_pam:(locus_inversion:20, locus_indel:(9,0))) 3. build () What is the expected output? What do you see instead? At the end of the 4th wagner build this error appears.... Error : File "sequence.ml", line 705, characters 8-14: Assertion failed Fatal error: exception Assert_failure("sequence.ml", 705, 8) Please use labels and text to provide additional information. May 13, 2009 issue 75 (tree output has two semi-colons at the end of the tree) commented on by loucrow - update; the tree file with the double semi-colon is actually two tree files, it's just that the trees were somehow concatenated and the semicolon of the first, was placed after both trees. update; the tree file with the double semi-colon is actually two tree files, it's just that the trees were somehow concatenated and the semicolon of the first, was placed after both trees. May 13, 2009 issue 75 (tree output has two semi-colons at the end of the tree) reported by loucrow - What steps will reproduce the problem? 1. Ran the following script using the GUI read ("/Users/Louise/Desktop/morph21a.ss") build (1000) swap () report("1000trees.tre", trees) exit () 2. When I read the data file and the tree file into an interactive console, I got the following message: Error: │ │ input tree 685 of file │ │ /Users/Louise/Documents/Arcoida/Thesis/1000trees.tre has the terminal │ │ Hyotissa_hyotis and there is no data loaded for it │ │ │ │Error: │ │ Failure("Data not found") 3. I checked the tree file and there was a double semi-colon after the 684th tree, just before the outgroup taxon Hyotissa hyotis appears in the next tree. I built the trees twice and got the same result. What version of the product are you using? On what operating system? POY 4.1.1, OSX Leopard What steps will reproduce the problem? 1. Ran the following script using the GUI read ("/Users/Louise/Desktop/morph21a.ss") build (1000) swap () report("1000trees.tre", trees) exit () 2. When I read the data file and the tree file into an interactive console, I got the following message: Error: │ │ input tree 685 of file │ │ /Users/Louise/Documents/Arcoida/Thesis/1000trees.tre has the terminal │ │ Hyotissa_hyotis and there is no data loaded for it │ │ │ │Error: │ │ Failure("Data not found") 3. I checked the tree file and there was a double semi-colon after the 684th tree, just before the outgroup taxon Hyotissa hyotis appears in the next tree. I built the trees twice and got the same result. What version of the product are you using? On what operating system? POY 4.1.1, OSX Leopard May 08, 2009 issue 74 (not_found error when reporting an implied alignment) Status changed by lynXiamen - changeset: XXX:4ec26b3e57c9 branch: release5-05-07 tag: tip user: lyn@YanBox.internal.amnh.org date: Wed May 06 17:09:36 2009 -0400 files: src/impliedAlignment.ml description: fix issue 74 symptom: not_found error when reporting an implied alignment Problem: in impliedAlignment.ml, function ancestor_breakinv changes the sequence of a clade when it should not Solution: when we are calculating the median, we should swap the sequence of two clades when necessary, but if we are not doing that, just pass the ancestor one along. Status: Fixed changeset: XXX:4ec26b3e57c9 branch: release5-05-07 tag: tip user: lyn@YanBox.internal.amnh.org date: Wed May 06 17:09:36 2009 -0400 files: src/impliedAlignment.ml description: fix issue 74 symptom: not_found error when reporting an implied alignment Problem: in impliedAlignment.ml, function ancestor_breakinv changes the sequence of a clade when it should not Solution: when we are calculating the median, we should swap the sequence of two clades when necessary, but if we are not doing that, just pass the ancestor one along. Status: Fixed Apr 25, 2009 issue 74 (not_found error when reporting an implied alignment) reported by me...@amnh.org - What steps will reproduce the problem? 1. run the script "breakinv_inv30.poy" in parallel (2 processors, ignore the first cd line) 2. 3. What is the expected output? What do you see instead? Expected and implied alignment to be generated...instead "Error: Not_found" Please use labels and text to provide additional information. What steps will reproduce the problem? 1. run the script "breakinv_inv30.poy" in parallel (2 processors, ignore the first cd line) 2. 3. What is the expected output? What do you see instead? Expected and implied alignment to be generated...instead "Error: Not_found" Please use labels and text to provide additional information. Apr 13, 2009 issue 73 (not getting consensus reports from a script) reported by paola.pedraza - What steps will reproduce the problem? 1. I'm failing to produce consensus trees and graphic consensus from an script using the interactive console. At the begining I thought that the consensus were not being reported because the analyses found only one most parsimonious tree. But, my report command doesn't work even when several MPT are found. However, if I ask the consensus trees and pdf to be reported on a separate line, and not along with the other reports I want, it does work. 2. 3. What is the expected output? What do you see instead? graphic consensus and consensus tree in parentethical format What version of the product are you using? On what operating system? 4.1.1 Please provide any additional information below. What steps will reproduce the problem? 1. I'm failing to produce consensus trees and graphic consensus from an script using the interactive console. At the begining I thought that the consensus were not being reported because the analyses found only one most parsimonious tree. But, my report command doesn't work even when several MPT are found. However, if I ask the consensus trees and pdf to be reported on a separate line, and not along with the other reports I want, it does work. 2. 3. What is the expected output? What do you see instead? graphic consensus and consensus tree in parentethical format What version of the product are you using? On what operating system? 4.1.1 Please provide any additional information below. Apr 09, 2009 issue 72 (Build error in Custom Alphabet files) changed by avaron - This problem was caused by an incorrect size in the transformation cost matrix in the input file m5.fas. The bug is that POY does not verify the consistency in the matrix size and the alphabet declared in input tcm. This has now been corrected in 9617d74d69bd for version 4.1.2. Status: Fixed Owner: avaron This problem was caused by an incorrect size in the transformation cost matrix in the input file m5.fas. The bug is that POY does not verify the consistency in the matrix size and the alphabet declared in input tcm. This has now been corrected in 9617d74d69bd for version 4.1.2. Status: Fixed Owner: avaron Apr 08, 2009 issue 72 (Build error in Custom Alphabet files) reported by me...@amnh.org - What steps will reproduce the problem? 1. read (custom_alphabet:("ca5.fas", "m5.fas")) 2. build () 3. What is the expected output? What do you see instead? expected output: 10 Wagner trees observed output: File "seqCS.ml", line 772, characters 12-18: Assertion failed Please use labels and text to provide additional information. What steps will reproduce the problem? 1. read (custom_alphabet:("ca5.fas", "m5.fas")) 2. build () 3. What is the expected output? What do you see instead? expected output: 10 Wagner trees observed output: File "seqCS.ml", line 772, characters 12-18: Assertion failed Please use labels and text to provide additional information. Apr 07, 2009 issue 70 (poy 4.1 GUI simple search for jackknife generates bootstraps) changed by avaron - Fixed in 4.1.1 Status: Fixed Labels: Type-Defect Fixed in 4.1.1 Status: Fixed Labels: Type-Defect Apr 07, 2009 issue 71 (terminals file: error yes, stopping no) changed by avaron - Fixed in 4.1.1 Status: Fixed Labels: Type-Defect Fixed in 4.1.1 Status: Fixed Labels: Type-Defect Feb 03, 2009 Repository synced up to r177 by avaron Jan 23, 2009 Repository synced up to r175 by avaron Older Dec 29, 2008 issue 71 (terminals file: error yes, stopping no) reported by loucrow - When using a terminals file, POY will not stop the run if it cannot read the terminals file. It will report an error but will continue on searching. It would be very helpful if POY would stop and not continue on with the run. Of course it is important to do test runs on my computer before I put something on the cluster, but it's a big pain in the derrier if I put something on and after 12 hours + I get results back with terminals included that I did not intend. Only then do I get the error file saying that POY could not load the terminals file. Perhaps there was a reason for not stopping the run, but if the user does not intend to run the analysis with all the taxa and does intend to do so with only some, then I think it would be better for the run to stop. What version of the product are you using? On what operating system? 4.1.1.ve1 Please provide any additional information below. When using a terminals file, POY will not stop the run if it cannot read the terminals file. It will report an error but will continue on searching. It would be very helpful if POY would stop and not continue on with the run. Of course it is important to do test runs on my computer before I put something on the cluster, but it's a big pain in the derrier if I put something on and after 12 hours + I get results back with terminals included that I did not intend. Only then do I get the error file saying that POY could not load the terminals file. Perhaps there was a reason for not stopping the run, but if the user does not intend to run the analysis with all the taxa and does intend to do so with only some, then I think it would be better for the run to stop. What version of the product are you using? On what operating system? 4.1.1.ve1 Please provide any additional information below. Nov 30, 2008 issue 70 (poy 4.1 GUI simple search for jackknife generates bootstraps) reported by loucrow - What steps will reproduce the problem? 1. the jackknife window of the GUI asks for bootstrap parameters, not jackknife parameters, therefore when you generate the script and report the supports, you are asking for bootstrap values and not jackknifes What version of the product are you using? On what operating system? POY 4.1, mac OSX Please provide any additional information below. This is following on from GG question to the POY group. I just checked out the GUI. What steps will reproduce the problem? 1. the jackknife window of the GUI asks for bootstrap parameters, not jackknife parameters, therefore when you generate the script and report the supports, you are asking for bootstrap values and not jackknifes What version of the product are you using? On what operating system? POY 4.1, mac OSX Please provide any additional information below. This is following on from GG question to the POY group. I just checked out the GUI. Sep 24, 2008 issue 69 (Large alphabet error with annotated dataset) Status changed by avaron - Vinh noted that the true problem was that make clean needed to be executed before make poy. This is a symptom of missing dependency rules in the Makefile. These have been corrected in 3c58ca5d805a (4.0.2899 will have the feature corrected). Status: Fixed Vinh noted that the true problem was that make clean needed to be executed before make poy. This is a symptom of missing dependency rules in the Makefile. These have been corrected in 3c58ca5d805a (4.0.2899 will have the feature corrected). Status: Fixed Sep 18, 2008 issue 69 (Large alphabet error with annotated dataset) reported by me...@amnh.org - What steps will reproduce the problem? 1. read (annotated:("deca_dup_si")) 2. build (1) 3. What is the expected output? What do you see instead? Expect output is 1 tree. Instead the error appears :Failure ("Apparently you are analyzing large alphabets. This version of POY was compiled without the --enable-large-alphabets option. To run this analysis you need to enable that option) What version of the product are you using? On what operating system? POY 4.0.3f0d16e64150+ MAC Leopard Please provide any additional information below. What steps will reproduce the problem? 1. read (annotated:("deca_dup_si")) 2. build (1) 3. What is the expected output? What do you see instead? Expect output is 1 tree. Instead the error appears :Failure ("Apparently you are analyzing large alphabets. This version of POY was compiled without the --enable-large-alphabets option. To run this analysis you need to enable that option) What version of the product are you using? On what operating system? POY 4.0.3f0d16e64150+ MAC Leopard Please provide any additional information below. Sep 11, 2008 issue 67 (diagnosis not reporting changes) Status changed by avaron - Fixed in 2889. To verify it update your checked-out copy of the repository and recompile. Status: Fixed Fixed in 2889. To verify it update your checked-out copy of the repository and recompile. Status: Fixed Sep 10, 2008 issue 68 (googlecode subversion repository is empty) Status changed by avaron - The repository is functional again. Status: Fixed The repository is functional again. Status: Fixed Sep 10, 2008 issue 67 (diagnosis not reporting changes) commented on by danjanies - Hi Andres reran with latest version of poy-mpi bmi.osu.edu/~janies/h5n1pb2239wed.tgz I am still evaluating the results with respect to pos 18XX - will get back to you. Dan Hi Andres reran with latest version of poy-mpi bmi.osu.edu/~janies/h5n1pb2239wed.tgz I am still evaluating the results with respect to pos 18XX - will get back to you. Dan Sep 09, 2008 issue 67 (diagnosis not reporting changes) commented on by danjanies - Andres Its the version I downloaded yesterday before the archive broke Information : Welcome to POY 4.0 RC, build 2744 "Pelletier"! compiled with parallel on, interface flat, graphics none Rerunning now to be sure and will send you the whole directory. Thanks Dan Andres Its the version I downloaded yesterday before the archive broke Information : Welcome to POY 4.0 RC, build 2744 "Pelletier"! compiled with parallel on, interface flat, graphics none Rerunning now to be sure and will send you the whole directory. Thanks Dan Sep 09, 2008 issue 67 (diagnosis not reporting changes) commented on by avaron - Ah, OK, let me check something else. Ah, OK, let me check something else. Sep 09, 2008 issue 67 (diagnosis not reporting changes) commented on by avaron - Dan what version of POY is this? I misread your initial message, but it says early 08 ... that means months old POY? I can't get a similar output with the latest version, everything looks normal here. Could you please try to reproduce with the latest version? Dan what version of POY is this? I misread your initial message, but it says early 08 ... that means months old POY? I can't get a similar output with the latest version, everything looks normal here. Could you please try to reproduce with the latest version? Sep 09, 2008 issue 67 (diagnosis not reporting changes) commented on by danjanies - <transformation Character="ImpliedAlignment2" Pos="1895" AncS="A" DescS="C" Type="Tv" Cost="1." Definite="true"/> i see that but its not correct the only states at that site are A and G looked in the alignment vicinity but nothing looks right. Also looked at all A to G and G to A changes and none are at 1895. Of all changes A to G or G to A there should be 8 total here is the apolist and a summary from paup and poy. see bmi.osu.edu/~janies/pos1985.zip Whats the discrepency? THANKS and if you want to take this to another forum thats fine....Dan <transformation Character="ImpliedAlignment2" Pos="1895" AncS="A" DescS="C" Type="Tv" Cost="1." Definite="true"/> i see that but its not correct the only states at that site are A and G looked in the alignment vicinity but nothing looks right. Also looked at all A to G and G to A changes and none are at 1895. Of all changes A to G or G to A there should be 8 total here is the apolist and a summary from paup and poy. see bmi.osu.edu/~janies/pos1985.zip Whats the discrepency? THANKS and if you want to take this to another forum thats fine....Dan Sep 09, 2008 issue 67 (diagnosis not reporting changes) commented on by danjanies - wait you see it in both temp.xml and transformed.xml ? wait you see it in both temp.xml and transformed.xml ? Sep 09, 2008 issue 67 (diagnosis not reporting changes) commented on by danjanies - Thanks so looks like its being missed by the xslt step? Dan Thanks so looks like its being missed by the xslt step? Dan Sep 09, 2008 issue 67 (diagnosis not reporting changes) commented on by avaron - The character is there ... line 39093 of results5e2fd5.xml. It's also in the xml representation of the tree with the corresponding optimization on every node that I checked. The character is there ... line 39093 of results5e2fd5.xml. It's also in the xml representation of the tree with the corresponding optimization on every node that I checked. Sep 09, 2008 issue 67 (diagnosis not reporting changes) commented on by danjanies - Hi Andres et al I ran tcm:(1,1) now I'm looking for a specific mutation that confers the ability of the virus to infect mammals. a G -> A transition (and some reversals) at aligned position 1895 counting from 1. I see it in the applied alignment but not in the tmp file or the xslt resulting xml. Whats wrong? Results in bmi.osu.edu/~janies/headtcm11.zip Thanks! Dan Hi Andres et al I ran tcm:(1,1) now I'm looking for a specific mutation that confers the ability of the virus to infect mammals. a G -> A transition (and some reversals) at aligned position 1895 counting from 1. I see it in the applied alignment but not in the tmp file or the xslt resulting xml. Whats wrong? Results in bmi.osu.edu/~janies/headtcm11.zip Thanks! Dan Sep 08, 2008 issue 66 (diagnosis not reporting changes) Status changed by avaron - Status: Duplicate Status: Duplicate Sep 08, 2008 issue 68 (googlecode subversion repository is empty) changed by avaron - Summary: googlecode subversion repository is empty Status: Accepted Summary: googlecode subversion repository is empty Status: Accepted Sep 08, 2008 issue 68 (compile prob in mpi) commented on by avaron - The subversion repository is having troubles, so it's down for now. The subversion repository is having troubles, so it's down for now. Sep 08, 2008 issue 68 (compile prob in mpi) commented on by avaron - Dan you have to include CC=mpicc in the configure step. Dan you have to include CC=mpicc in the configure step. Sep 08, 2008 issue 68 (compile prob in mpi) reported by danjanies - Hi Andres I got this to downlowd - svn http://poy4.googlecode.com/svn/trunk/ poy4-read-only its flaky however currently svn co http://poy4.googlecode.com/svn/trunk/ poy4-read-only svn: URL 'http://poy4.googlecode.com/svn/trunk' doesn't exist [danjanies@head ~]$ svn checkout http://poy4.googlecode.com/svn/trunk/ poy4-read-only svn: URL 'http://poy4.googlecode.com/svn/trunk' doesn't exist in any case ./configure -enable-xslt -enable-interface=flat -enable-long-sequences worked fine through compile on Linux version 2.6.18-6-mckinley (Debian 2.6.18.dfsg.1-18etch1) (waldi@debian.org) (gcc version 4.1.2 20061115 (prerelease) (Debian 4.1.1-21)) #1 SMP Mon Feb 11 11:47:35 UTC 2008 and Linux version 2.6.18-92.1.10.el5 (mockbuild@builder10.centos.org) (gcc version 4.1.2 20071124 (Red Hat 4.1.2-42)) #1 SMP Tue Aug 5 07:42:41 EDT 2008 testing sequential binary now.... however with ./configure -enable-xslt -enable-interface=flat -enable-long-sequences -enable-mpi I'm getting ../ocamlmpi//libcamlmpi.a(comm.o): In function `caml_mpi_cart_coords': /home/danjanies/poy4-read-only/ocamlmpi/comm.c:134: undefined reference to `MPI_Cartdim_get' /home/danjanies/poy4-read-only/ocamlmpi/comm.c:136: undefined reference to `MPI_Cart_coords' ../ocamlmpi//libcamlmpi.a(comm.o): In function `caml_mpi_cart_rank': /home/danjanies/poy4-read-only/ocamlmpi/comm.c:123: undefined reference to `MPI_Cart_rank' ../ocamlmpi//libcamlmpi.a(comm.o): In function `caml_mpi_dims_create': /home/danjanies/poy4-read-only/ocamlmpi/comm.c:109: undefined reference to `MPI_Dims_create' /home/danjanies/poy4-read-only/ocamlmpi/comm.c:109: undefined reference to `MPI_Dims_create' ../ocamlmpi//libcamlmpi.a(comm.o): In function `caml_mpi_comm_compare': /home/danjanies/poy4-read-only/ocamlmpi/comm.c:67: undefined reference to `MPI_Comm_compare' ../ocamlmpi//libcamlmpi.a(comm.o): In function `caml_mpi_comm_rank': /home/danjanies/poy4-read-only/ocamlmpi/comm.c:60: undefined reference to `MPI_Comm_rank' ../ocamlmpi//libcamlmpi.a(comm.o): In function `caml_mpi_comm_size': /home/danjanies/poy4-read-only/ocamlmpi/comm.c:53: undefined reference to `MPI_Comm_size' ../ocamlmpi//libcamlmpi.a(comm.o): In function `caml_mpi_intercomm_create': /home/danjanies/poy4-read-only/ocamlmpi/comm.c:155: undefined reference to `MPI_Intercomm_create' ../ocamlmpi//libcamlmpi.a(comm.o): In function `caml_mpi_comm_create': /home/danjanies/poy4-read-only/ocamlmpi/comm.c:146: undefined reference to `MPI_Comm_create' ../ocamlmpi//libcamlmpi.a(comm.o): In function `caml_mpi_cart_create': /home/danjanies/poy4-read-only/ocamlmpi/comm.c:94: undefined reference to `MPI_Cart_create' ../ocamlmpi//libcamlmpi.a(comm.o): In function `caml_mpi_comm_split': /home/danjanies/poy4-read-only/ocamlmpi/comm.c:74: undefined reference to `MPI_Comm_split' ../ocamlmpi//libcamlmpi.a(comm.o): In function `caml_mpi_finalize_comm': /home/danjanies/poy4-read-only/ocamlmpi/comm.c:26: undefined reference to `MPI_Comm_free' ../ocamlmpi//libcamlmpi.a(msgs.o): In function `caml_mpi_receive_floatarray': /home/danjanies/poy4-read-only/ocamlmpi/msgs.c:196: undefined reference to `MPI_Recv' ../ocamlmpi//libcamlmpi.a(msgs.o): In function `caml_mpi_receive_intarray': /home/danjanies/poy4-read-only/ocamlmpi/msgs.c:175: undefined reference to `MPI_Recv' ../ocamlmpi//libcamlmpi.a(msgs.o): In function `caml_mpi_receive_int': /home/danjanies/poy4-read-only/ocamlmpi/msgs.c:166: undefined reference to `MPI_Recv' ../ocamlmpi//libcamlmpi.a(msgs.o): In function `caml_mpi_receive_float': /home/danjanies/poy4-read-only/ocamlmpi/msgs.c:185: undefined reference to `MPI_Recv' ../ocamlmpi//libcamlmpi.a(msgs.o): In function `caml_mpi_receive': /home/danjanies/poy4-read-only/ocamlmpi/msgs.c:152: undefined reference to `MPI_Recv' ../ocamlmpi//libcamlmpi.a(msgs.o): In function `caml_mpi_iprobe': /home/danjanies/poy4-read-only/ocamlmpi/msgs.c:129: undefined reference to `MPI_Iprobe' ../ocamlmpi//libcamlmpi.a(msgs.o): In function `caml_mpi_probe': /home/danjanies/poy4-read-only/ocamlmpi/msgs.c:110: undefined reference to `MPI_Probe' /home/danjanies/poy4-read-only/ocamlmpi/msgs.c:111: undefined reference to `MPI_Get_count' ../ocamlmpi//libcamlmpi.a(msgs.o): In function `caml_mpi_send_float': /home/danjanies/poy4-read-only/ocamlmpi/msgs.c:97: undefined reference to `MPI_Send' ../ocamlmpi//libcamlmpi.a(msgs.o): In function `caml_mpi_send_intarray': /home/danjanies/poy4-read-only/ocamlmpi/msgs.c:87: undefined reference to `MPI_Send' ../ocamlmpi//libcamlmpi.a(msgs.o): In function `caml_mpi_send_int': /home/danjanies/poy4-read-only/ocamlmpi/msgs.c:81: undefined reference to `MPI_Send' ../ocamlmpi//libcamlmpi.a(msgs.o): In function `caml_mpi_send': /home/danjanies/poy4-read-only/ocamlmpi/msgs.c:41: undefined reference to `MPI_Send' ../ocamlmpi//libcamlmpi.a(msgs.o): In function `caml_mpi_isend': /home/danjanies/poy4-read-only/ocamlmpi/msgs.c:65: undefined reference to `MPI_Isend' /home/danjanies/poy4-read-only/ocamlmpi/msgs.c:69: undefined reference to `MPI_Test' ../ocamlmpi//libcamlmpi.a(collcomm.o): In function `caml_mpi_scan_floatarray': /home/danjanies/poy4-read-only/ocamlmpi/collcomm.c:406: undefined reference to `MPI_Scan' ../ocamlmpi//libcamlmpi.a(collcomm.o): In function `caml_mpi_scan_int': /home/danjanies/poy4-read-only/ocamlmpi/collcomm.c:371: undefined reference to `MPI_Scan' ../ocamlmpi//libcamlmpi.a(collcomm.o): In function `caml_mpi_scan_float': /home/danjanies/poy4-read-only/ocamlmpi/collcomm.c:395: undefined reference to `MPI_Scan' ../ocamlmpi//libcamlmpi.a(collcomm.o): In function `caml_mpi_scan_intarray': /home/danjanies/poy4-read-only/ocamlmpi/collcomm.c:382: undefined reference to `MPI_Scan' ../ocamlmpi//libcamlmpi.a(collcomm.o): In function `caml_mpi_allreduce_floatarray': /home/danjanies/poy4-read-only/ocamlmpi/collcomm.c:357: undefined reference to `MPI_Allreduce' ../ocamlmpi//libcamlmpi.a(collcomm.o): In function `caml_mpi_allreduce_float': /home/danjanies/poy4-read-only/ocamlmpi/collcomm.c:345: undefined reference to `MPI_Allreduce' ../ocamlmpi//libcamlmpi.a(collcomm.o): In function `caml_mpi_allreduce_intarray': /home/danjanies/poy4-read-only/ocamlmpi/collcomm.c:332: undefined reference to `MPI_Allreduce' ../ocamlmpi//libcamlmpi.a(collcomm.o): In function `caml_mpi_allreduce_int': /home/danjanies/poy4-read-only/ocamlmpi/collcomm.c:320: undefined reference to `MPI_Allreduce' ../ocamlmpi//libcamlmpi.a(collcomm.o): In function `caml_mpi_reduce_floatarray': /home/danjanies/poy4-read-only/ocamlmpi/collcomm.c:307: undefined reference to `MPI_Reduce' ../ocamlmpi//libcamlmpi.a(collcomm.o): In function `caml_mpi_reduce_float': /home/danjanies/poy4-read-only/ocamlmpi/collcomm.c:295: undefined reference to `MPI_Reduce' ../ocamlmpi//libcamlmpi.a(collcomm.o): In function `caml_mpi_reduce_int': /home/danjanies/poy4-read-only/ocamlmpi/collcomm.c:267: undefined reference to `MPI_Reduce' ../ocamlmpi//libcamlmpi.a(collcomm.o): In function `caml_mpi_reduce_intarray': /home/danjanies/poy4-read-only/ocamlmpi/collcomm.c:281: undefined reference to `MPI_Reduce' /home/danjanies/poy4-read-only/ocamlmpi/collcomm.c:286: undefined reference to `MPI_Comm_rank' ../ocamlmpi//libcamlmpi.a(collcomm.o): In function `caml_mpi_allgather_float': /home/danjanies/poy4-read-only/ocamlmpi/collcomm.c:249: undefined reference to `MPI_Allgather' ../ocamlmpi//libcamlmpi.a(collcomm.o): In function `caml_mpi_allgather_intarray': /home/danjanies/poy4-read-only/ocamlmpi/collcomm.c:236: undefined reference to `MPI_Allgather' ../ocamlmpi//libcamlmpi.a(collcomm.o): In function `caml_mpi_allgather_int': /home/danjanies/poy4-read-only/ocamlmpi/collcomm.c:227: undefined reference to `MPI_Allgather' ../ocamlmpi//libcamlmpi.a(collcomm.o): In function `caml_mpi_allgather': /home/danjanies/poy4-read-only/ocamlmpi/collcomm.c:217: undefined reference to `MPI_Allgatherv' ../ocamlmpi//libcamlmpi.a(collcomm.o): In function `caml_mpi_gather_float': /home/danjanies/poy4-read-only/ocamlmpi/collcomm.c:201: undefined reference to `MPI_Gather' ../ocamlmpi//libcamlmpi.a(collcomm.o): In function `caml_mpi_gather_intarray': /home/danjanies/poy4-read-only/ocamlmpi/collcomm.c:188: undefined reference to `MPI_Gather' ../ocamlmpi//libcamlmpi.a(collcomm.o): In function `caml_mpi_gather_int': /home/danjanies/poy4-read-only/ocamlmpi/collcomm.c:178: undefined reference to `MPI_Gather' ../ocamlmpi//libcamlmpi.a(collcomm.o): In function `caml_mpi_gather': /home/danjanies/poy4-read-only/ocamlmpi/collcomm.c:166: undefined reference to `MPI_Gatherv' ../ocamlmpi//libcamlmpi.a(collcomm.o): In function `caml_mpi_scatter_floatarray': /home/danjanies/poy4-read-only/ocamlmpi/collcomm.c:150: undefined reference to `MPI_Scatter' ../ocamlmpi//libcamlmpi.a(collcomm.o): In function `caml_mpi_scatter_intarray': /home/danjanies/poy4-read-only/ocamlmpi/collcomm.c:136: undefined reference to `MPI_Scatter' ../ocamlmpi//libcamlmpi.a(collcomm.o): In function `caml_mpi_scatter_float': /home/danjanies/poy4-read-only/ocamlmpi/collcomm.c:126: undefined reference to `MPI_Scatter' ../ocamlmpi//libcamlmpi.a(collcomm.o): In function `caml_mpi_scatter_int': /home/danjanies/poy4-read-only/ocamlmpi/collcomm.c:115: undefined reference to `MPI_Scatter' ../ocamlmpi//libcamlmpi.a(collcomm.o): In function `caml_mpi_scatter': /home/danjanies/poy4-read-only/ocamlmpi/collcomm.c:101: undefined reference to `MPI_Scatterv' ../ocamlmpi//libcamlmpi.a(collcomm.o): In function `caml_mpi_broadcast_floatarray': /home/danjanies/poy4-read-only/ocamlmpi/collcomm.c:66: undefined reference to `MPI_Bcast' ../ocamlmpi//libcamlmpi.a(collcomm.o): In function `caml_mpi_broadcast_intarray': /home/danjanies/poy4-read-only/ocamlmpi/collcomm.c:57: undefined reference to `MPI_Bcast' ../ocamlmpi//libcamlmpi.a(collcomm.o): In function `caml_mpi_broadcast_float': /home/danjanies/poy4-read-only/ocamlmpi/collcomm.c:51: undefined reference to `MPI_Bcast' ../ocamlmpi//libcamlmpi.a(collcomm.o): In function `caml_mpi_broadcast_int': /home/danjanies/poy4-read-only/ocamlmpi/collcomm.c:44: undefined reference to `MPI_Bcast' ../ocamlmpi//libcamlmpi.a(collcomm.o): In function `caml_mpi_broadcast': /home/danjanies/poy4-read-only/ocamlmpi/collcomm.c:36: undefined reference to `MPI_Bcast' ../ocamlmpi//libcamlmpi.a(collcomm.o): In function `caml_mpi_barrier': /home/danjanies/poy4-read-only/ocamlmpi/collcomm.c:28: undefined reference to `MPI_Barrier' ../ocamlmpi//libcamlmpi.a(groups.o): In function `caml_mpi_group_translate_ranks': /home/danjanies/poy4-read-only/ocamlmpi/groups.c:61: undefined reference to `MPI_Group_translate_ranks' /home/danjanies/poy4-read-only/ocamlmpi/groups.c:61: undefined reference to `MPI_Group_translate_ranks' ../ocamlmpi//libcamlmpi.a(groups.o): In function `caml_mpi_group_rank': /home/danjanies/poy4-read-only/ocamlmpi/groups.c:48: undefined reference to `MPI_Group_rank' ../ocamlmpi//libcamlmpi.a(groups.o): In function `caml_mpi_group_size': /home/danjanies/poy4-read-only/ocamlmpi/groups.c:41: undefined reference to `MPI_Group_size' ../ocamlmpi//libcamlmpi.a(groups.o): In function `caml_mpi_group_range_excl': /home/danjanies/poy4-read-only/ocamlmpi/groups.c:158: undefined reference to `MPI_Group_range_excl' ../ocamlmpi//libcamlmpi.a(groups.o): In function `caml_mpi_group_range_incl': /home/danjanies/poy4-read-only/ocamlmpi/groups.c:147: undefined reference to `MPI_Group_range_incl' ../ocamlmpi//libcamlmpi.a(groups.o): In function `caml_mpi_group_excl': /home/danjanies/poy4-read-only/ocamlmpi/groups.c:119: undefined reference to `MPI_Group_excl' ../ocamlmpi//libcamlmpi.a(groups.o): In function `caml_mpi_group_incl': /home/danjanies/poy4-read-only/ocamlmpi/groups.c:106: undefined reference to `MPI_Group_incl' ../ocamlmpi//libcamlmpi.a(groups.o): In function `caml_mpi_group_intersection': /home/danjanies/poy4-read-only/ocamlmpi/groups.c:94: undefined reference to `MPI_Group_intersection' ../ocamlmpi//libcamlmpi.a(groups.o): In function `caml_mpi_group_difference': /home/danjanies/poy4-read-only/ocamlmpi/groups.c:87: undefined reference to `MPI_Group_difference' ../ocamlmpi//libcamlmpi.a(groups.o): In function `caml_mpi_group_union': /home/danjanies/poy4-read-only/ocamlmpi/groups.c:80: undefined reference to `MPI_Group_union' ../ocamlmpi//libcamlmpi.a(groups.o): In function `caml_mpi_comm_group': /home/danjanies/poy4-read-only/ocamlmpi/groups.c:73: undefined reference to `MPI_Comm_group' ../ocamlmpi//libcamlmpi.a(groups.o): In function `caml_mpi_finalize_group': /home/danjanies/poy4-read-only/ocamlmpi/groups.c:26: undefined reference to `MPI_Group_free' collect2: ld returned 1 exit status Error during linking make[2]: * [help.txt] Error 2 make[2]: Leaving directory `/home/danjanies/poy4-read-only/src' make[1]: * [depend] Error 2 make[1]: Leaving directory `/home/danjanies/poy4-read-only' make: * [all] Error 2 have not changed mpich install on the cluster whats wrong? THANKS! Dan Hi Andres I got this to downlowd - svn http://poy4.googlecode.com/svn/trunk/ poy4-read-only its flaky however currently svn co http://poy4.googlecode.com/svn/trunk/ poy4-read-only svn: URL 'http://poy4.googlecode.com/svn/trunk' doesn't exist [danjanies@head ~]$ svn checkout http://poy4.googlecode.com/svn/trunk/ poy4-read-only svn: URL 'http://poy4.googlecode.com/svn/trunk' doesn't exist in any case ./configure -enable-xslt -enable-interface=flat -enable-long-sequences worked fine through compile on Linux version 2.6.18-6-mckinley (Debian 2.6.18.dfsg.1-18etch1) (waldi@debian.org) (gcc version 4.1.2 20061115 (prerelease) (Debian 4.1.1-21)) #1 SMP Mon Feb 11 11:47:35 UTC 2008 and Linux version 2.6.18-92.1.10.el5 (mockbuild@builder10.centos.org) (gcc version 4.1.2 20071124 (Red Hat 4.1.2-42)) #1 SMP Tue Aug 5 07:42:41 EDT 2008 testing sequential binary now.... however with ./configure -enable-xslt -enable-interface=flat -enable-long-sequences -enable-mpi I'm getting ../ocamlmpi//libcamlmpi.a(comm.o): In function `caml_mpi_cart_coords': /home/danjanies/poy4-read-only/ocamlmpi/comm.c:134: undefined reference to `MPI_Cartdim_get' /home/danjanies/poy4-read-only/ocamlmpi/comm.c:136: undefined reference to `MPI_Cart_coords' ../ocamlmpi//libcamlmpi.a(comm.o): In function `caml_mpi_cart_rank': /home/danjanies/poy4-read-only/ocamlmpi/comm.c:123: undefined reference to `MPI_Cart_rank' ../ocamlmpi//libcamlmpi.a(comm.o): In function `caml_mpi_dims_create': /home/danjanies/poy4-read-only/ocamlmpi/comm.c:109: undefined reference to `MPI_Dims_create' /home/danjanies/poy4-read-only/ocamlmpi/comm.c:109: undefined reference to `MPI_Dims_create' ../ocamlmpi//libcamlmpi.a(comm.o): In function `caml_mpi_comm_compare': /home/danjanies/poy4-read-only/ocamlmpi/comm.c:67: undefined reference to `MPI_Comm_compare' ../ocamlmpi//libcamlmpi.a(comm.o): In function `caml_mpi_comm_rank': /home/danjanies/poy4-read-only/ocamlmpi/comm.c:60: undefined reference to `MPI_Comm_rank' ../ocamlmpi//libcamlmpi.a(comm.o): In function `caml_mpi_comm_size': /home/danjanies/poy4-read-only/ocamlmpi/comm.c:53: undefined reference to `MPI_Comm_size' ../ocamlmpi//libcamlmpi.a(comm.o): In function `caml_mpi_intercomm_create': /home/danjanies/poy4-read-only/ocamlmpi/comm.c:155: undefined reference to `MPI_Intercomm_create' ../ocamlmpi//libcamlmpi.a(comm.o): In function `caml_mpi_comm_create': /home/danjanies/poy4-read-only/ocamlmpi/comm.c:146: undefined reference to `MPI_Comm_create' ../ocamlmpi//libcamlmpi.a(comm.o): In function `caml_mpi_cart_create': /home/danjanies/poy4-read-only/ocamlmpi/comm.c:94: undefined reference to `MPI_Cart_create' ../ocamlmpi//libcamlmpi.a(comm.o): In function `caml_mpi_comm_split': /home/danjanies/poy4-read-only/ocamlmpi/comm.c:74: undefined reference to `MPI_Comm_split' ../ocamlmpi//libcamlmpi.a(comm.o): In function `caml_mpi_finalize_comm': /home/danjanies/poy4-read-only/ocamlmpi/comm.c:26: undefined reference to `MPI_Comm_free' ../ocamlmpi//libcamlmpi.a(msgs.o): In function `caml_mpi_receive_floatarray': /home/danjanies/poy4-read-only/ocamlmpi/msgs.c:196: undefined reference to `MPI_Recv' ../ocamlmpi//libcamlmpi.a(msgs.o): In function `caml_mpi_receive_intarray': /home/danjanies/poy4-read-only/ocamlmpi/msgs.c:175: undefined reference to `MPI_Recv' ../ocamlmpi//libcamlmpi.a(msgs.o): In function `caml_mpi_receive_int': /home/danjanies/poy4-read-only/ocamlmpi/msgs.c:166: undefined reference to `MPI_Recv' ../ocamlmpi//libcamlmpi.a(msgs.o): In function `caml_mpi_receive_float': /home/danjanies/poy4-read-only/ocamlmpi/msgs.c:185: undefined reference to `MPI_Recv' ../ocamlmpi//libcamlmpi.a(msgs.o): In function `caml_mpi_receive': /home/danjanies/poy4-read-only/ocamlmpi/msgs.c:152: undefined reference to `MPI_Recv' ../ocamlmpi//libcamlmpi.a(msgs.o): In function `caml_mpi_iprobe': /home/danjanies/poy4-read-only/ocamlmpi/msgs.c:129: undefined reference to `MPI_Iprobe' ../ocamlmpi//libcamlmpi.a(msgs.o): In function `caml_mpi_probe': /home/danjanies/poy4-read-only/ocamlmpi/msgs.c:110: undefined reference to `MPI_Probe' /home/danjanies/poy4-read-only/ocamlmpi/msgs.c:111: undefined reference to `MPI_Get_count' ../ocamlmpi//libcamlmpi.a(msgs.o): In function `caml_mpi_send_float': /home/danjanies/poy4-read-only/ocamlmpi/msgs.c:97: undefined reference to `MPI_Send' ../ocamlmpi//libcamlmpi.a(msgs.o): In function `caml_mpi_send_intarray': /home/danjanies/poy4-read-only/ocamlmpi/msgs.c:87: undefined reference to `MPI_Send' ../ocamlmpi//libcamlmpi.a(msgs.o): In function `caml_mpi_send_int': /home/danjanies/poy4-read-only/ocamlmpi/msgs.c:81: undefined reference to `MPI_Send' ../ocamlmpi//libcamlmpi.a(msgs.o): In function `caml_mpi_send': /home/danjanies/poy4-read-only/ocamlmpi/msgs.c:41: undefined reference to `MPI_Send' ../ocamlmpi//libcamlmpi.a(msgs.o): In function `caml_mpi_isend': /home/danjanies/poy4-read-only/ocamlmpi/msgs.c:65: undefined reference to `MPI_Isend' /home/danjanies/poy4-read-only/ocamlmpi/msgs.c:69: undefined reference to `MPI_Test' ../ocamlmpi//libcamlmpi.a(collcomm.o): In function `caml_mpi_scan_floatarray': /home/danjanies/poy4-read-only/ocamlmpi/collcomm.c:406: undefined reference to `MPI_Scan' ../ocamlmpi//libcamlmpi.a(collcomm.o): In function `caml_mpi_scan_int': /home/danjanies/poy4-read-only/ocamlmpi/collcomm.c:371: undefined reference to `MPI_Scan' ../ocamlmpi//libcamlmpi.a(collcomm.o): In function `caml_mpi_scan_float': /home/danjanies/poy4-read-only/ocamlmpi/collcomm.c:395: undefined reference to `MPI_Scan' ../ocamlmpi//libcamlmpi.a(collcomm.o): In function `caml_mpi_scan_intarray': /home/danjanies/poy4-read-only/ocamlmpi/collcomm.c:382: undefined reference to `MPI_Scan' ../ocamlmpi//libcamlmpi.a(collcomm.o): In function `caml_mpi_allreduce_floatarray': /home/danjanies/poy4-read-only/ocamlmpi/collcomm.c:357: undefined reference to `MPI_Allreduce' ../ocamlmpi//libcamlmpi.a(collcomm.o): In function `caml_mpi_allreduce_float': /home/danjanies/poy4-read-only/ocamlmpi/collcomm.c:345: undefined reference to `MPI_Allreduce' ../ocamlmpi//libcamlmpi.a(collcomm.o): In function `caml_mpi_allreduce_intarray': /home/danjanies/poy4-read-only/ocamlmpi/collcomm.c:332: undefined reference to `MPI_Allreduce' ../ocamlmpi//libcamlmpi.a(collcomm.o): In function `caml_mpi_allreduce_int': /home/danjanies/poy4-read-only/ocamlmpi/collcomm.c:320: undefined reference to `MPI_Allreduce' ../ocamlmpi//libcamlmpi.a(collcomm.o): In function `caml_mpi_reduce_floatarray': /home/danjanies/poy4-read-only/ocamlmpi/collcomm.c:307: undefined reference to `MPI_Reduce' ../ocamlmpi//libcamlmpi.a(collcomm.o): In function `caml_mpi_reduce_float': /home/danjanies/poy4-read-only/ocamlmpi/collcomm.c:295: undefined reference to `MPI_Reduce' ../ocamlmpi//libcamlmpi.a(collcomm.o): In function `caml_mpi_reduce_int': /home/danjanies/poy4-read-only/ocamlmpi/collcomm.c:267: undefined reference to `MPI_Reduce' ../ocamlmpi//libcamlmpi.a(collcomm.o): In function `caml_mpi_reduce_intarray': /home/danjanies/poy4-read-only/ocamlmpi/collcomm.c:281: undefined reference to `MPI_Reduce' /home/danjanies/poy4-read-only/ocamlmpi/collcomm.c:286: undefined reference to `MPI_Comm_rank' ../ocamlmpi//libcamlmpi.a(collcomm.o): In function `caml_mpi_allgather_float': /home/danjanies/poy4-read-only/ocamlmpi/collcomm.c:249: undefined reference to `MPI_Allgather' ../ocamlmpi//libcamlmpi.a(collcomm.o): In function `caml_mpi_allgather_intarray': /home/danjanies/poy4-read-only/ocamlmpi/collcomm.c:236: undefined reference to `MPI_Allgather' ../ocamlmpi//libcamlmpi.a(collcomm.o): In function `caml_mpi_allgather_int': /home/danjanies/poy4-read-only/ocamlmpi/collcomm.c:227: undefined reference to `MPI_Allgather' ../ocamlmpi//libcamlmpi.a(collcomm.o): In function `caml_mpi_allgather': /home/danjanies/poy4-read-only/ocamlmpi/collcomm.c:217: undefined reference to `MPI_Allgatherv' ../ocamlmpi//libcamlmpi.a(collcomm.o): In function `caml_mpi_gather_float': /home/danjanies/poy4-read-only/ocamlmpi/collcomm.c:201: undefined reference to `MPI_Gather' ../ocamlmpi//libcamlmpi.a(collcomm.o): In function `caml_mpi_gather_intarray': /home/danjanies/poy4-read-only/ocamlmpi/collcomm.c:188: undefined reference to `MPI_Gather' ../ocamlmpi//libcamlmpi.a(collcomm.o): In function `caml_mpi_gather_int': /home/danjanies/poy4-read-only/ocamlmpi/collcomm.c:178: undefined reference to `MPI_Gather' ../ocamlmpi//libcamlmpi.a(collcomm.o): In function `caml_mpi_gather': /home/danjanies/poy4-read-only/ocamlmpi/collcomm.c:166: undefined reference to `MPI_Gatherv' ../ocamlmpi//libcamlmpi.a(collcomm.o): In function `caml_mpi_scatter_floatarray': /home/danjanies/poy4-read-only/ocamlmpi/collcomm.c:150: undefined reference to `MPI_Scatter' ../ocamlmpi//libcamlmpi.a(collcomm.o): In function `caml_mpi_scatter_intarray': /home/danjanies/poy4-read-only/ocamlmpi/collcomm.c:136: undefined reference to `MPI_Scatter' ../ocamlmpi//libcamlmpi.a(collcomm.o): In function `caml_mpi_scatter_float': /home/danjanies/poy4-read-only/ocamlmpi/collcomm.c:126: undefined reference to `MPI_Scatter' ../ocamlmpi//libcamlmpi.a(collcomm.o): In function `caml_mpi_scatter_int': /home/danjanies/poy4-read-only/ocamlmpi/collcomm.c:115: undefined reference to `MPI_Scatter' ../ocamlmpi//libcamlmpi.a(collcomm.o): In function `caml_mpi_scatter': /home/danjanies/poy4-read-only/ocamlmpi/collcomm.c:101: undefined reference to `MPI_Scatterv' ../ocamlmpi//libcamlmpi.a(collcomm.o): In function `caml_mpi_broadcast_floatarray': /home/danjanies/poy4-read-only/ocamlmpi/collcomm.c:66: undefined reference to `MPI_Bcast' ../ocamlmpi//libcamlmpi.a(collcomm.o): In function `caml_mpi_broadcast_intarray': /home/danjanies/poy4-read-only/ocamlmpi/collcomm.c:57: undefined reference to `MPI_Bcast' ../ocamlmpi//libcamlmpi.a(collcomm.o): In function `caml_mpi_broadcast_float': /home/danjanies/poy4-read-only/ocamlmpi/collcomm.c:51: undefined reference to `MPI_Bcast' ../ocamlmpi//libcamlmpi.a(collcomm.o): In function `caml_mpi_broadcast_int': /home/danjanies/poy4-read-only/ocamlmpi/collcomm.c:44: undefined reference to `MPI_Bcast' ../ocamlmpi//libcamlmpi.a(collcomm.o): In function `caml_mpi_broadcast': /home/danjanies/poy4-read-only/ocamlmpi/collcomm.c:36: undefined reference to `MPI_Bcast' ../ocamlmpi//libcamlmpi.a(collcomm.o): In function `caml_mpi_barrier': /home/danjanies/poy4-read-only/ocamlmpi/collcomm.c:28: undefined reference to `MPI_Barrier' ../ocamlmpi//libcamlmpi.a(groups.o): In function `caml_mpi_group_translate_ranks': /home/danjanies/poy4-read-only/ocamlmpi/groups.c:61: undefined reference to `MPI_Group_translate_ranks' /home/danjanies/poy4-read-only/ocamlmpi/groups.c:61: undefined reference to `MPI_Group_translate_ranks' ../ocamlmpi//libcamlmpi.a(groups.o): In function `caml_mpi_group_rank': /home/danjanies/poy4-read-only/ocamlmpi/groups.c:48: undefined reference to `MPI_Group_rank' ../ocamlmpi//libcamlmpi.a(groups.o): In function `caml_mpi_group_size': /home/danjanies/poy4-read-only/ocamlmpi/groups.c:41: undefined reference to `MPI_Group_size' ../ocamlmpi//libcamlmpi.a(groups.o): In function `caml_mpi_group_range_excl': /home/danjanies/poy4-read-only/ocamlmpi/groups.c:158: undefined reference to `MPI_Group_range_excl' ../ocamlmpi//libcamlmpi.a(groups.o): In function `caml_mpi_group_range_incl': /home/danjanies/poy4-read-only/ocamlmpi/groups.c:147: undefined reference to `MPI_Group_range_incl' ../ocamlmpi//libcamlmpi.a(groups.o): In function `caml_mpi_group_excl': /home/danjanies/poy4-read-only/ocamlmpi/groups.c:119: undefined reference to `MPI_Group_excl' ../ocamlmpi//libcamlmpi.a(groups.o): In function `caml_mpi_group_incl': /home/danjanies/poy4-read-only/ocamlmpi/groups.c:106: undefined reference to `MPI_Group_incl' ../ocamlmpi//libcamlmpi.a(groups.o): In function `caml_mpi_group_intersection': /home/danjanies/poy4-read-only/ocamlmpi/groups.c:94: undefined reference to `MPI_Group_intersection' ../ocamlmpi//libcamlmpi.a(groups.o): In function `caml_mpi_group_difference': /home/danjanies/poy4-read-only/ocamlmpi/groups.c:87: undefined reference to `MPI_Group_difference' ../ocamlmpi//libcamlmpi.a(groups.o): In function `caml_mpi_group_union': /home/danjanies/poy4-read-only/ocamlmpi/groups.c:80: undefined reference to `MPI_Group_union' ../ocamlmpi//libcamlmpi.a(groups.o): In function `caml_mpi_comm_group': /home/danjanies/poy4-read-only/ocamlmpi/groups.c:73: undefined reference to `MPI_Comm_group' ../ocamlmpi//libcamlmpi.a(groups.o): In function `caml_mpi_finalize_group': /home/danjanies/poy4-read-only/ocamlmpi/groups.c:26: undefined reference to `MPI_Group_free' collect2: ld returned 1 exit status Error during linking make[2]: * [help.txt] Error 2 make[2]: Leaving directory `/home/danjanies/poy4-read-only/src' make[1]: * [depend] Error 2 make[1]: Leaving directory `/home/danjanies/poy4-read-only' make: * [all] Error 2 have not changed mpich install on the cluster whats wrong? THANKS! Dan Sep 08, 2008 r134 (Removed all the contents. ) committed by avaron - Removed all the contents. Removed all the contents. Sep 08, 2008 issue 67 (diagnosis not reporting changes) commented on by avaron - What cost matrix are you using? The encoding of the characters will change depending on the matrix. For instance, if the cost matrix is tcm:(1,1), then yes, there will be one character per column in the alignment. But if the cost matrix is tcm:(1,2) then there will also be a separate character with weight 2 corresponding to the individual indels (the present/absent character you see). Moreover, if there is a tcm of the form tcm:(3,1) gap_opening:3 then there will be also a separate character corresponding to the blocks of indels, with weight 3. What cost matrix are you using? The encoding of the characters will change depending on the matrix. For instance, if the cost matrix is tcm:(1,1), then yes, there will be one character per column in the alignment. But if the cost matrix is tcm:(1,2) then there will also be a separate character with weight 2 corresponding to the individual indels (the present/absent character you see). Moreover, if there is a tcm of the form tcm:(3,1) gap_opening:3 then there will be also a separate character corresponding to the blocks of indels, with weight 3. Sep 08, 2008 issue 67 (diagnosis not reporting changes) reported by danjanies - What steps will reproduce the problem? 1. Diagnosis of the dataset in any version of poy4 compiled early 08 2. basic dataset is here bmi.osu.edu/~janies/h5n1pb2239diagsimple.tar What is the expected output? What do you see instead? for example a G -> A transition (and maybe some reversals) at aligned position 1884 (is this 1883 in poys index)? here is an optimization of the character using the poy implied alignment and tree bmi.osu.edu/~janies/diagproblem.zip What version of the product are you using? On what operating system? tried the following Linux version 2.6.18-92.1.10.el5 POY version 4.0, Copyright (C) Linux version 2.6.18-6-mckinley POY 4.0 RC, build 2744 "Pelletier"! Please provide any additional information below. I see <transformation Character="ImpliedAlignment2:4531" AncS="absent" DescS="present" Type="non-additive character" Cost="1." Definite="true"/> in the xml but there are only nucleotide characters. I see "pos" tag missing in some lines of the xml. the above could be related to the xslt step (e.g. a style sheet that is out of date with the diag output). I include the temp file as well in bmi.osu.edu/~janies/h5n1pb2239diagsimple.tar I checked the temp file and see no mentions of a mutation at pos 1883. I wil keep working with new and old versions of poy. Thanks! Dan What steps will reproduce the problem? 1. Diagnosis of the dataset in any version of poy4 compiled early 08 2. basic dataset is here bmi.osu.edu/~janies/h5n1pb2239diagsimple.tar What is the expected output? What do you see instead? for example a G -> A transition (and maybe some reversals) at aligned position 1884 (is this 1883 in poys index)? here is an optimization of the character using the poy implied alignment and tree bmi.osu.edu/~janies/diagproblem.zip What version of the product are you using? On what operating system? tried the following Linux version 2.6.18-92.1.10.el5 POY version 4.0, Copyright (C) Linux version 2.6.18-6-mckinley POY 4.0 RC, build 2744 "Pelletier"! Please provide any additional information below. I see <transformation Character="ImpliedAlignment2:4531" AncS="absent" DescS="present" Type="non-additive character" Cost="1." Definite="true"/> in the xml but there are only nucleotide characters. I see "pos" tag missing in some lines of the xml. the above could be related to the xslt step (e.g. a style sheet that is out of date with the diag output). I include the temp file as well in bmi.osu.edu/~janies/h5n1pb2239diagsimple.tar I checked the temp file and see no mentions of a mutation at pos 1883. I wil keep working with new and old versions of poy. Thanks! Dan Aug 14, 2008 r128 committed by avaron Aug 14, 2008 issue 64 (Add report (searchstats)) Status changed by avaron - Added in 4.0.2885 Status: Fixed Added in 4.0.2885 Status: Fixed Aug 13, 2008 r126 (Tag trunk as build_4_0_2884. ) committed by avaron - Tag trunk as build_4_0_2884. Tag trunk as build_4_0_2884. Aug 13, 2008 r125 committed by avaron Aug 06, 2008 issue 65 (Error in iterative documentation) Status changed by me...@amnh.org - Fixed in version 10c64a59e008 Status: Fixed Fixed in version 10c64a59e008 Status: Fixed Aug 06, 2008 issue 63 (inconsistence with example of jackknife in the manual) Status changed by me...@amnh.org - Status: Fixed Status: Fixed Aug 06, 2008 issue 65 (Error in iterative documentation) changed by me...@amnh.org - Status: Accepted Owner: me...@amnh.org Status: Accepted Owner: me...@amnh.org

issue 68 (compile prob in mpi) reported by danjanies - Hi Andres I got this to downlowd - svn http://poy4.googlecode.com/svn/trunk/ poy4-read-only its flaky however currently svn co http://poy4.googlecode.com/svn/trunk/ poy4-read-only svn: URL 'http://poy4.googlecode.com/svn/trunk' doesn't exist [danjanies@head ~]$ svn checkout http://poy4.googlecode.com/svn/trunk/ poy4-read-only svn: URL 'http://poy4.googlecode.com/svn/trunk' doesn't exist in any case ./configure -enable-xslt -enable-interface=flat -enable-long-sequences worked fine through compile on Linux version 2.6.18-6-mckinley (Debian 2.6.18.dfsg.1-18etch1) (waldi@debian.org) (gcc version 4.1.2 20061115 (prerelease) (Debian 4.1.1-21)) #1 SMP Mon Feb 11 11:47:35 UTC 2008 and Linux version 2.6.18-92.1.10.el5 (mockbuild@builder10.centos.org) (gcc version 4.1.2 20071124 (Red Hat 4.1.2-42)) #1 SMP Tue Aug 5 07:42:41 EDT 2008 testing sequential binary now.... however with ./configure -enable-xslt -enable-interface=flat -enable-long-sequences -enable-mpi I'm getting ../ocamlmpi//libcamlmpi.a(comm.o): In function `caml_mpi_cart_coords': /home/danjanies/poy4-read-only/ocamlmpi/comm.c:134: undefined reference to `MPI_Cartdim_get' /home/danjanies/poy4-read-only/ocamlmpi/comm.c:136: undefined reference to `MPI_Cart_coords' ../ocamlmpi//libcamlmpi.a(comm.o): In function `caml_mpi_cart_rank': /home/danjanies/poy4-read-only/ocamlmpi/comm.c:123: undefined reference to `MPI_Cart_rank' ../ocamlmpi//libcamlmpi.a(comm.o): In function `caml_mpi_dims_create': /home/danjanies/poy4-read-only/ocamlmpi/comm.c:109: undefined reference to `MPI_Dims_create' /home/danjanies/poy4-read-only/ocamlmpi/comm.c:109: undefined reference to `MPI_Dims_create' ../ocamlmpi//libcamlmpi.a(comm.o): In function `caml_mpi_comm_compare': /home/danjanies/poy4-read-only/ocamlmpi/comm.c:67: undefined reference to `MPI_Comm_compare' ../ocamlmpi//libcamlmpi.a(comm.o): In function `caml_mpi_comm_rank': /home/danjanies/poy4-read-only/ocamlmpi/comm.c:60: undefined reference to `MPI_Comm_rank' ../ocamlmpi//libcamlmpi.a(comm.o): In function `caml_mpi_comm_size': /home/danjanies/poy4-read-only/ocamlmpi/comm.c:53: undefined reference to `MPI_Comm_size' ../ocamlmpi//libcamlmpi.a(comm.o): In function `caml_mpi_intercomm_create': /home/danjanies/poy4-read-only/ocamlmpi/comm.c:155: undefined reference to `MPI_Intercomm_create' ../ocamlmpi//libcamlmpi.a(comm.o): In function `caml_mpi_comm_create': /home/danjanies/poy4-read-only/ocamlmpi/comm.c:146: undefined reference to `MPI_Comm_create' ../ocamlmpi//libcamlmpi.a(comm.o): In function `caml_mpi_cart_create': /home/danjanies/poy4-read-only/ocamlmpi/comm.c:94: undefined reference to `MPI_Cart_create' ../ocamlmpi//libcamlmpi.a(comm.o): In function `caml_mpi_comm_split': /home/danjanies/poy4-read-only/ocamlmpi/comm.c:74: undefined reference to `MPI_Comm_split' ../ocamlmpi//libcamlmpi.a(comm.o): In function `caml_mpi_finalize_comm': /home/danjanies/poy4-read-only/ocamlmpi/comm.c:26: undefined reference to `MPI_Comm_free' ../ocamlmpi//libcamlmpi.a(msgs.o): In function `caml_mpi_receive_floatarray': /home/danjanies/poy4-read-only/ocamlmpi/msgs.c:196: undefined reference to `MPI_Recv' ../ocamlmpi//libcamlmpi.a(msgs.o): In function `caml_mpi_receive_intarray': /home/danjanies/poy4-read-only/ocamlmpi/msgs.c:175: undefined reference to `MPI_Recv' ../ocamlmpi//libcamlmpi.a(msgs.o): In function `caml_mpi_receive_int': /home/danjanies/poy4-read-only/ocamlmpi/msgs.c:166: undefined reference to `MPI_Recv' ../ocamlmpi//libcamlmpi.a(msgs.o): In function `caml_mpi_receive_float': /home/danjanies/poy4-read-only/ocamlmpi/msgs.c:185: undefined reference to `MPI_Recv' ../ocamlmpi//libcamlmpi.a(msgs.o): In function `caml_mpi_receive': /home/danjanies/poy4-read-only/ocamlmpi/msgs.c:152: undefined reference to `MPI_Recv' ../ocamlmpi//libcamlmpi.a(msgs.o): In function `caml_mpi_iprobe': /home/danjanies/poy4-read-only/ocamlmpi/msgs.c:129: undefined reference to `MPI_Iprobe' ../ocamlmpi//libcamlmpi.a(msgs.o): In function `caml_mpi_probe': /home/danjanies/poy4-read-only/ocamlmpi/msgs.c:110: undefined reference to `MPI_Probe' /home/danjanies/poy4-read-only/ocamlmpi/msgs.c:111: undefined reference to `MPI_Get_count' ../ocamlmpi//libcamlmpi.a(msgs.o): In function `caml_mpi_send_float': /home/danjanies/poy4-read-only/ocamlmpi/msgs.c:97: undefined reference to `MPI_Send' ../ocamlmpi//libcamlmpi.a(msgs.o): In function `caml_mpi_send_intarray': /home/danjanies/poy4-read-only/ocamlmpi/msgs.c:87: undefined reference to `MPI_Send' ../ocamlmpi//libcamlmpi.a(msgs.o): In function `caml_mpi_send_int': /home/danjanies/poy4-read-only/ocamlmpi/msgs.c:81: undefined reference to `MPI_Send' ../ocamlmpi//libcamlmpi.a(msgs.o): In function `caml_mpi_send': /home/danjanies/poy4-read-only/ocamlmpi/msgs.c:41: undefined reference to `MPI_Send' ../ocamlmpi//libcamlmpi.a(msgs.o): In function `caml_mpi_isend': /home/danjanies/poy4-read-only/ocamlmpi/msgs.c:65: undefined reference to `MPI_Isend' /home/danjanies/poy4-read-only/ocamlmpi/msgs.c:69: undefined reference to `MPI_Test' ../ocamlmpi//libcamlmpi.a(collcomm.o): In function `caml_mpi_scan_floatarray': /home/danjanies/poy4-read-only/ocamlmpi/collcomm.c:406: undefined reference to `MPI_Scan' ../ocamlmpi//libcamlmpi.a(collcomm.o): In function `caml_mpi_scan_int': /home/danjanies/poy4-read-only/ocamlmpi/collcomm.c:371: undefined reference to `MPI_Scan' ../ocamlmpi//libcamlmpi.a(collcomm.o): In function `caml_mpi_scan_float': /home/danjanies/poy4-read-only/ocamlmpi/collcomm.c:395: undefined reference to `MPI_Scan' ../ocamlmpi//libcamlmpi.a(collcomm.o): In function `caml_mpi_scan_intarray': /home/danjanies/poy4-read-only/ocamlmpi/collcomm.c:382: undefined reference to `MPI_Scan' ../ocamlmpi//libcamlmpi.a(collcomm.o): In function `caml_mpi_allreduce_floatarray': /home/danjanies/poy4-read-only/ocamlmpi/collcomm.c:357: undefined reference to `MPI_Allreduce' ../ocamlmpi//libcamlmpi.a(collcomm.o): In function `caml_mpi_allreduce_float': /home/danjanies/poy4-read-only/ocamlmpi/collcomm.c:345: undefined reference to `MPI_Allreduce' ../ocamlmpi//libcamlmpi.a(collcomm.o): In function `caml_mpi_allreduce_intarray': /home/danjanies/poy4-read-only/ocamlmpi/collcomm.c:332: undefined reference to `MPI_Allreduce' ../ocamlmpi//libcamlmpi.a(collcomm.o): In function `caml_mpi_allreduce_int': /home/danjanies/poy4-read-only/ocamlmpi/collcomm.c:320: undefined reference to `MPI_Allreduce' ../ocamlmpi//libcamlmpi.a(collcomm.o): In function `caml_mpi_reduce_floatarray': /home/danjanies/poy4-read-only/ocamlmpi/collcomm.c:307: undefined reference to `MPI_Reduce' ../ocamlmpi//libcamlmpi.a(collcomm.o): In function `caml_mpi_reduce_float': /home/danjanies/poy4-read-only/ocamlmpi/collcomm.c:295: undefined reference to `MPI_Reduce' ../ocamlmpi//libcamlmpi.a(collcomm.o): In function `caml_mpi_reduce_int': /home/danjanies/poy4-read-only/ocamlmpi/collcomm.c:267: undefined reference to `MPI_Reduce' ../ocamlmpi//libcamlmpi.a(collcomm.o): In function `caml_mpi_reduce_intarray': /home/danjanies/poy4-read-only/ocamlmpi/collcomm.c:281: undefined reference to `MPI_Reduce' /home/danjanies/poy4-read-only/ocamlmpi/collcomm.c:286: undefined reference to `MPI_Comm_rank' ../ocamlmpi//libcamlmpi.a(collcomm.o): In function `caml_mpi_allgather_float': /home/danjanies/poy4-read-only/ocamlmpi/collcomm.c:249: undefined reference to `MPI_Allgather' ../ocamlmpi//libcamlmpi.a(collcomm.o): In function `caml_mpi_allgather_intarray': /home/danjanies/poy4-read-only/ocamlmpi/collcomm.c:236: undefined reference to `MPI_Allgather' ../ocamlmpi//libcamlmpi.a(collcomm.o): In function `caml_mpi_allgather_int': /home/danjanies/poy4-read-only/ocamlmpi/collcomm.c:227: undefined reference to `MPI_Allgather' ../ocamlmpi//libcamlmpi.a(collcomm.o): In function `caml_mpi_allgather': /home/danjanies/poy4-read-only/ocamlmpi/collcomm.c:217: undefined reference to `MPI_Allgatherv' ../ocamlmpi//libcamlmpi.a(collcomm.o): In function `caml_mpi_gather_float': /home/danjanies/poy4-read-only/ocamlmpi/collcomm.c:201: undefined reference to `MPI_Gather' ../ocamlmpi//libcamlmpi.a(collcomm.o): In function `caml_mpi_gather_intarray': /home/danjanies/poy4-read-only/ocamlmpi/collcomm.c:188: undefined reference to `MPI_Gather' ../ocamlmpi//libcamlmpi.a(collcomm.o): In function `caml_mpi_gather_int': /home/danjanies/poy4-read-only/ocamlmpi/collcomm.c:178: undefined reference to `MPI_Gather' ../ocamlmpi//libcamlmpi.a(collcomm.o): In function `caml_mpi_gather': /home/danjanies/poy4-read-only/ocamlmpi/collcomm.c:166: undefined reference to `MPI_Gatherv' ../ocamlmpi//libcamlmpi.a(collcomm.o): In function `caml_mpi_scatter_floatarray': /home/danjanies/poy4-read-only/ocamlmpi/collcomm.c:150: undefined reference to `MPI_Scatter' ../ocamlmpi//libcamlmpi.a(collcomm.o): In function `caml_mpi_scatter_intarray': /home/danjanies/poy4-read-only/ocamlmpi/collcomm.c:136: undefined reference to `MPI_Scatter' ../ocamlmpi//libcamlmpi.a(collcomm.o): In function `caml_mpi_scatter_float': /home/danjanies/poy4-read-only/ocamlmpi/collcomm.c:126: undefined reference to `MPI_Scatter' ../ocamlmpi//libcamlmpi.a(collcomm.o): In function `caml_mpi_scatter_int': /home/danjanies/poy4-read-only/ocamlmpi/collcomm.c:115: undefined reference to `MPI_Scatter' ../ocamlmpi//libcamlmpi.a(collcomm.o): In function `caml_mpi_scatter': /home/danjanies/poy4-read-only/ocamlmpi/collcomm.c:101: undefined reference to `MPI_Scatterv' ../ocamlmpi//libcamlmpi.a(collcomm.o): In function `caml_mpi_broadcast_floatarray': /home/danjanies/poy4-read-only/ocamlmpi/collcomm.c:66: undefined reference to `MPI_Bcast' ../ocamlmpi//libcamlmpi.a(collcomm.o): In function `caml_mpi_broadcast_intarray': /home/danjanies/poy4-read-only/ocamlmpi/collcomm.c:57: undefined reference to `MPI_Bcast' ../ocamlmpi//libcamlmpi.a(collcomm.o): In function `caml_mpi_broadcast_float': /home/danjanies/poy4-read-only/ocamlmpi/collcomm.c:51: undefined reference to `MPI_Bcast' ../ocamlmpi//libcamlmpi.a(collcomm.o): In function `caml_mpi_broadcast_int': /home/danjanies/poy4-read-only/ocamlmpi/collcomm.c:44: undefined reference to `MPI_Bcast' ../ocamlmpi//libcamlmpi.a(collcomm.o): In function `caml_mpi_broadcast': /home/danjanies/poy4-read-only/ocamlmpi/collcomm.c:36: undefined reference to `MPI_Bcast' ../ocamlmpi//libcamlmpi.a(collcomm.o): In function `caml_mpi_barrier': /home/danjanies/poy4-read-only/ocamlmpi/collcomm.c:28: undefined reference to `MPI_Barrier' ../ocamlmpi//libcamlmpi.a(groups.o): In function `caml_mpi_group_translate_ranks': /home/danjanies/poy4-read-only/ocamlmpi/groups.c:61: undefined reference to `MPI_Group_translate_ranks' /home/danjanies/poy4-read-only/ocamlmpi/groups.c:61: undefined reference to `MPI_Group_translate_ranks' ../ocamlmpi//libcamlmpi.a(groups.o): In function `caml_mpi_group_rank': /home/danjanies/poy4-read-only/ocamlmpi/groups.c:48: undefined reference to `MPI_Group_rank' ../ocamlmpi//libcamlmpi.a(groups.o): In function `caml_mpi_group_size': /home/danjanies/poy4-read-only/ocamlmpi/groups.c:41: undefined reference to `MPI_Group_size' ../ocamlmpi//libcamlmpi.a(groups.o): In function `caml_mpi_group_range_excl': /home/danjanies/poy4-read-only/ocamlmpi/groups.c:158: undefined reference to `MPI_Group_range_excl' ../ocamlmpi//libcamlmpi.a(groups.o): In function `caml_mpi_group_range_incl': /home/danjanies/poy4-read-only/ocamlmpi/groups.c:147: undefined reference to `MPI_Group_range_incl' ../ocamlmpi//libcamlmpi.a(groups.o): In function `caml_mpi_group_excl': /home/danjanies/poy4-read-only/ocamlmpi/groups.c:119: undefined reference to `MPI_Group_excl' ../ocamlmpi//libcamlmpi.a(groups.o): In function `caml_mpi_group_incl': /home/danjanies/poy4-read-only/ocamlmpi/groups.c:106: undefined reference to `MPI_Group_incl' ../ocamlmpi//libcamlmpi.a(groups.o): In function `caml_mpi_group_intersection': /home/danjanies/poy4-read-only/ocamlmpi/groups.c:94: undefined reference to `MPI_Group_intersection' ../ocamlmpi//libcamlmpi.a(groups.o): In function `caml_mpi_group_difference': /home/danjanies/poy4-read-only/ocamlmpi/groups.c:87: undefined reference to `MPI_Group_difference' ../ocamlmpi//libcamlmpi.a(groups.o): In function `caml_mpi_group_union': /home/danjanies/poy4-read-only/ocamlmpi/groups.c:80: undefined reference to `MPI_Group_union' ../ocamlmpi//libcamlmpi.a(groups.o): In function `caml_mpi_comm_group': /home/danjanies/poy4-read-only/ocamlmpi/groups.c:73: undefined reference to `MPI_Comm_group' ../ocamlmpi//libcamlmpi.a(groups.o): In function `caml_mpi_finalize_group': /home/danjanies/poy4-read-only/ocamlmpi/groups.c:26: undefined reference to `MPI_Group_free' collect2: ld returned 1 exit status Error during linking make[2]: *** [help.txt] Error 2 make[2]: Leaving directory `/home/danjanies/poy4-read-only/src' make[1]: *** [depend] Error 2 make[1]: Leaving directory `/home/danjanies/poy4-read-only' make: *** [all] Error 2 have not changed mpich install on the cluster whats wrong? THANKS! Dan

Hi Andres I got this to downlowd - svn http://poy4.googlecode.com/svn/trunk/ poy4-read-only its flaky however currently svn co http://poy4.googlecode.com/svn/trunk/ poy4-read-only svn: URL 'http://poy4.googlecode.com/svn/trunk' doesn't exist [danjanies@head ~]$ svn checkout http://poy4.googlecode.com/svn/trunk/ poy4-read-only svn: URL 'http://poy4.googlecode.com/svn/trunk' doesn't exist in any case ./configure -enable-xslt -enable-interface=flat -enable-long-sequences worked fine through compile on Linux version 2.6.18-6-mckinley (Debian 2.6.18.dfsg.1-18etch1) (waldi@debian.org) (gcc version 4.1.2 20061115 (prerelease) (Debian 4.1.1-21)) #1 SMP Mon Feb 11 11:47:35 UTC 2008 and Linux version 2.6.18-92.1.10.el5 (mockbuild@builder10.centos.org) (gcc version 4.1.2 20071124 (Red Hat 4.1.2-42)) #1 SMP Tue Aug 5 07:42:41 EDT 2008 testing sequential binary now.... however with ./configure -enable-xslt -enable-interface=flat -enable-long-sequences -enable-mpi I'm getting ../ocamlmpi//libcamlmpi.a(comm.o): In function `caml_mpi_cart_coords': /home/danjanies/poy4-read-only/ocamlmpi/comm.c:134: undefined reference to `MPI_Cartdim_get' /home/danjanies/poy4-read-only/ocamlmpi/comm.c:136: undefined reference to `MPI_Cart_coords' ../ocamlmpi//libcamlmpi.a(comm.o): In function `caml_mpi_cart_rank': /home/danjanies/poy4-read-only/ocamlmpi/comm.c:123: undefined reference to `MPI_Cart_rank' ../ocamlmpi//libcamlmpi.a(comm.o): In function `caml_mpi_dims_create': /home/danjanies/poy4-read-only/ocamlmpi/comm.c:109: undefined reference to `MPI_Dims_create' /home/danjanies/poy4-read-only/ocamlmpi/comm.c:109: undefined reference to `MPI_Dims_create' ../ocamlmpi//libcamlmpi.a(comm.o): In function `caml_mpi_comm_compare': /home/danjanies/poy4-read-only/ocamlmpi/comm.c:67: undefined reference to `MPI_Comm_compare' ../ocamlmpi//libcamlmpi.a(comm.o): In function `caml_mpi_comm_rank': /home/danjanies/poy4-read-only/ocamlmpi/comm.c:60: undefined reference to `MPI_Comm_rank' ../ocamlmpi//libcamlmpi.a(comm.o): In function `caml_mpi_comm_size': /home/danjanies/poy4-read-only/ocamlmpi/comm.c:53: undefined reference to `MPI_Comm_size' ../ocamlmpi//libcamlmpi.a(comm.o): In function `caml_mpi_intercomm_create': /home/danjanies/poy4-read-only/ocamlmpi/comm.c:155: undefined reference to `MPI_Intercomm_create' ../ocamlmpi//libcamlmpi.a(comm.o): In function `caml_mpi_comm_create': /home/danjanies/poy4-read-only/ocamlmpi/comm.c:146: undefined reference to `MPI_Comm_create' ../ocamlmpi//libcamlmpi.a(comm.o): In function `caml_mpi_cart_create': /home/danjanies/poy4-read-only/ocamlmpi/comm.c:94: undefined reference to `MPI_Cart_create' ../ocamlmpi//libcamlmpi.a(comm.o): In function `caml_mpi_comm_split': /home/danjanies/poy4-read-only/ocamlmpi/comm.c:74: undefined reference to `MPI_Comm_split' ../ocamlmpi//libcamlmpi.a(comm.o): In function `caml_mpi_finalize_comm': /home/danjanies/poy4-read-only/ocamlmpi/comm.c:26: undefined reference to `MPI_Comm_free' ../ocamlmpi//libcamlmpi.a(msgs.o): In function `caml_mpi_receive_floatarray': /home/danjanies/poy4-read-only/ocamlmpi/msgs.c:196: undefined reference to `MPI_Recv' ../ocamlmpi//libcamlmpi.a(msgs.o): In function `caml_mpi_receive_intarray': /home/danjanies/poy4-read-only/ocamlmpi/msgs.c:175: undefined reference to `MPI_Recv' ../ocamlmpi//libcamlmpi.a(msgs.o): In function `caml_mpi_receive_int': /home/danjanies/poy4-read-only/ocamlmpi/msgs.c:166: undefined reference to `MPI_Recv' ../ocamlmpi//libcamlmpi.a(msgs.o): In function `caml_mpi_receive_float': /home/danjanies/poy4-read-only/ocamlmpi/msgs.c:185: undefined reference to `MPI_Recv' ../ocamlmpi//libcamlmpi.a(msgs.o): In function `caml_mpi_receive': /home/danjanies/poy4-read-only/ocamlmpi/msgs.c:152: undefined reference to `MPI_Recv' ../ocamlmpi//libcamlmpi.a(msgs.o): In function `caml_mpi_iprobe': /home/danjanies/poy4-read-only/ocamlmpi/msgs.c:129: undefined reference to `MPI_Iprobe' ../ocamlmpi//libcamlmpi.a(msgs.o): In function `caml_mpi_probe': /home/danjanies/poy4-read-only/ocamlmpi/msgs.c:110: undefined reference to `MPI_Probe' /home/danjanies/poy4-read-only/ocamlmpi/msgs.c:111: undefined reference to `MPI_Get_count' ../ocamlmpi//libcamlmpi.a(msgs.o): In function `caml_mpi_send_float': /home/danjanies/poy4-read-only/ocamlmpi/msgs.c:97: undefined reference to `MPI_Send' ../ocamlmpi//libcamlmpi.a(msgs.o): In function `caml_mpi_send_intarray': /home/danjanies/poy4-read-only/ocamlmpi/msgs.c:87: undefined reference to `MPI_Send' ../ocamlmpi//libcamlmpi.a(msgs.o): In function `caml_mpi_send_int': /home/danjanies/poy4-read-only/ocamlmpi/msgs.c:81: undefined reference to `MPI_Send' ../ocamlmpi//libcamlmpi.a(msgs.o): In function `caml_mpi_send': /home/danjanies/poy4-read-only/ocamlmpi/msgs.c:41: undefined reference to `MPI_Send' ../ocamlmpi//libcamlmpi.a(msgs.o): In function `caml_mpi_isend': /home/danjanies/poy4-read-only/ocamlmpi/msgs.c:65: undefined reference to `MPI_Isend' /home/danjanies/poy4-read-only/ocamlmpi/msgs.c:69: undefined reference to `MPI_Test' ../ocamlmpi//libcamlmpi.a(collcomm.o): In function `caml_mpi_scan_floatarray': /home/danjanies/poy4-read-only/ocamlmpi/collcomm.c:406: undefined reference to `MPI_Scan' ../ocamlmpi//libcamlmpi.a(collcomm.o): In function `caml_mpi_scan_int': /home/danjanies/poy4-read-only/ocamlmpi/collcomm.c:371: undefined reference to `MPI_Scan' ../ocamlmpi//libcamlmpi.a(collcomm.o): In function `caml_mpi_scan_float': /home/danjanies/poy4-read-only/ocamlmpi/collcomm.c:395: undefined reference to `MPI_Scan' ../ocamlmpi//libcamlmpi.a(collcomm.o): In function `caml_mpi_scan_intarray': /home/danjanies/poy4-read-only/ocamlmpi/collcomm.c:382: undefined reference to `MPI_Scan' ../ocamlmpi//libcamlmpi.a(collcomm.o): In function `caml_mpi_allreduce_floatarray': /home/danjanies/poy4-read-only/ocamlmpi/collcomm.c:357: undefined reference to `MPI_Allreduce' ../ocamlmpi//libcamlmpi.a(collcomm.o): In function `caml_mpi_allreduce_float': /home/danjanies/poy4-read-only/ocamlmpi/collcomm.c:345: undefined reference to `MPI_Allreduce' ../ocamlmpi//libcamlmpi.a(collcomm.o): In function `caml_mpi_allreduce_intarray': /home/danjanies/poy4-read-only/ocamlmpi/collcomm.c:332: undefined reference to `MPI_Allreduce' ../ocamlmpi//libcamlmpi.a(collcomm.o): In function `caml_mpi_allreduce_int': /home/danjanies/poy4-read-only/ocamlmpi/collcomm.c:320: undefined reference to `MPI_Allreduce' ../ocamlmpi//libcamlmpi.a(collcomm.o): In function `caml_mpi_reduce_floatarray': /home/danjanies/poy4-read-only/ocamlmpi/collcomm.c:307: undefined reference to `MPI_Reduce' ../ocamlmpi//libcamlmpi.a(collcomm.o): In function `caml_mpi_reduce_float': /home/danjanies/poy4-read-only/ocamlmpi/collcomm.c:295: undefined reference to `MPI_Reduce' ../ocamlmpi//libcamlmpi.a(collcomm.o): In function `caml_mpi_reduce_int': /home/danjanies/poy4-read-only/ocamlmpi/collcomm.c:267: undefined reference to `MPI_Reduce' ../ocamlmpi//libcamlmpi.a(collcomm.o): In function `caml_mpi_reduce_intarray': /home/danjanies/poy4-read-only/ocamlmpi/collcomm.c:281: undefined reference to `MPI_Reduce' /home/danjanies/poy4-read-only/ocamlmpi/collcomm.c:286: undefined reference to `MPI_Comm_rank' ../ocamlmpi//libcamlmpi.a(collcomm.o): In function `caml_mpi_allgather_float': /home/danjanies/poy4-read-only/ocamlmpi/collcomm.c:249: undefined reference to `MPI_Allgather' ../ocamlmpi//libcamlmpi.a(collcomm.o): In function `caml_mpi_allgather_intarray': /home/danjanies/poy4-read-only/ocamlmpi/collcomm.c:236: undefined reference to `MPI_Allgather' ../ocamlmpi//libcamlmpi.a(collcomm.o): In function `caml_mpi_allgather_int': /home/danjanies/poy4-read-only/ocamlmpi/collcomm.c:227: undefined reference to `MPI_Allgather' ../ocamlmpi//libcamlmpi.a(collcomm.o): In function `caml_mpi_allgather': /home/danjanies/poy4-read-only/ocamlmpi/collcomm.c:217: undefined reference to `MPI_Allgatherv' ../ocamlmpi//libcamlmpi.a(collcomm.o): In function `caml_mpi_gather_float': /home/danjanies/poy4-read-only/ocamlmpi/collcomm.c:201: undefined reference to `MPI_Gather' ../ocamlmpi//libcamlmpi.a(collcomm.o): In function `caml_mpi_gather_intarray': /home/danjanies/poy4-read-only/ocamlmpi/collcomm.c:188: undefined reference to `MPI_Gather' ../ocamlmpi//libcamlmpi.a(collcomm.o): In function `caml_mpi_gather_int': /home/danjanies/poy4-read-only/ocamlmpi/collcomm.c:178: undefined reference to `MPI_Gather' ../ocamlmpi//libcamlmpi.a(collcomm.o): In function `caml_mpi_gather': /home/danjanies/poy4-read-only/ocamlmpi/collcomm.c:166: undefined reference to `MPI_Gatherv' ../ocamlmpi//libcamlmpi.a(collcomm.o): In function `caml_mpi_scatter_floatarray': /home/danjanies/poy4-read-only/ocamlmpi/collcomm.c:150: undefined reference to `MPI_Scatter' ../ocamlmpi//libcamlmpi.a(collcomm.o): In function `caml_mpi_scatter_intarray': /home/danjanies/poy4-read-only/ocamlmpi/collcomm.c:136: undefined reference to `MPI_Scatter' ../ocamlmpi//libcamlmpi.a(collcomm.o): In function `caml_mpi_scatter_float': /home/danjanies/poy4-read-only/ocamlmpi/collcomm.c:126: undefined reference to `MPI_Scatter' ../ocamlmpi//libcamlmpi.a(collcomm.o): In function `caml_mpi_scatter_int': /home/danjanies/poy4-read-only/ocamlmpi/collcomm.c:115: undefined reference to `MPI_Scatter' ../ocamlmpi//libcamlmpi.a(collcomm.o): In function `caml_mpi_scatter': /home/danjanies/poy4-read-only/ocamlmpi/collcomm.c:101: undefined reference to `MPI_Scatterv' ../ocamlmpi//libcamlmpi.a(collcomm.o): In function `caml_mpi_broadcast_floatarray': /home/danjanies/poy4-read-only/ocamlmpi/collcomm.c:66: undefined reference to `MPI_Bcast' ../ocamlmpi//libcamlmpi.a(collcomm.o): In function `caml_mpi_broadcast_intarray': /home/danjanies/poy4-read-only/ocamlmpi/collcomm.c:57: undefined reference to `MPI_Bcast' ../ocamlmpi//libcamlmpi.a(collcomm.o): In function `caml_mpi_broadcast_float': /home/danjanies/poy4-read-only/ocamlmpi/collcomm.c:51: undefined reference to `MPI_Bcast' ../ocamlmpi//libcamlmpi.a(collcomm.o): In function `caml_mpi_broadcast_int': /home/danjanies/poy4-read-only/ocamlmpi/collcomm.c:44: undefined reference to `MPI_Bcast' ../ocamlmpi//libcamlmpi.a(collcomm.o): In function `caml_mpi_broadcast': /home/danjanies/poy4-read-only/ocamlmpi/collcomm.c:36: undefined reference to `MPI_Bcast' ../ocamlmpi//libcamlmpi.a(collcomm.o): In function `caml_mpi_barrier': /home/danjanies/poy4-read-only/ocamlmpi/collcomm.c:28: undefined reference to `MPI_Barrier' ../ocamlmpi//libcamlmpi.a(groups.o): In function `caml_mpi_group_translate_ranks': /home/danjanies/poy4-read-only/ocamlmpi/groups.c:61: undefined reference to `MPI_Group_translate_ranks' /home/danjanies/poy4-read-only/ocamlmpi/groups.c:61: undefined reference to `MPI_Group_translate_ranks' ../ocamlmpi//libcamlmpi.a(groups.o): In function `caml_mpi_group_rank': /home/danjanies/poy4-read-only/ocamlmpi/groups.c:48: undefined reference to `MPI_Group_rank' ../ocamlmpi//libcamlmpi.a(groups.o): In function `caml_mpi_group_size': /home/danjanies/poy4-read-only/ocamlmpi/groups.c:41: undefined reference to `MPI_Group_size' ../ocamlmpi//libcamlmpi.a(groups.o): In function `caml_mpi_group_range_excl': /home/danjanies/poy4-read-only/ocamlmpi/groups.c:158: undefined reference to `MPI_Group_range_excl' ../ocamlmpi//libcamlmpi.a(groups.o): In function `caml_mpi_group_range_incl': /home/danjanies/poy4-read-only/ocamlmpi/groups.c:147: undefined reference to `MPI_Group_range_incl' ../ocamlmpi//libcamlmpi.a(groups.o): In function `caml_mpi_group_excl': /home/danjanies/poy4-read-only/ocamlmpi/groups.c:119: undefined reference to `MPI_Group_excl' ../ocamlmpi//libcamlmpi.a(groups.o): In function `caml_mpi_group_incl': /home/danjanies/poy4-read-only/ocamlmpi/groups.c:106: undefined reference to `MPI_Group_incl' ../ocamlmpi//libcamlmpi.a(groups.o): In function `caml_mpi_group_intersection': /home/danjanies/poy4-read-only/ocamlmpi/groups.c:94: undefined reference to `MPI_Group_intersection' ../ocamlmpi//libcamlmpi.a(groups.o): In function `caml_mpi_group_difference': /home/danjanies/poy4-read-only/ocamlmpi/groups.c:87: undefined reference to `MPI_Group_difference' ../ocamlmpi//libcamlmpi.a(groups.o): In function `caml_mpi_group_union': /home/danjanies/poy4-read-only/ocamlmpi/groups.c:80: undefined reference to `MPI_Group_union' ../ocamlmpi//libcamlmpi.a(groups.o): In function `caml_mpi_comm_group': /home/danjanies/poy4-read-only/ocamlmpi/groups.c:73: undefined reference to `MPI_Comm_group' ../ocamlmpi//libcamlmpi.a(groups.o): In function `caml_mpi_finalize_group': /home/danjanies/poy4-read-only/ocamlmpi/groups.c:26: undefined reference to `MPI_Group_free' collect2: ld returned 1 exit status Error during linking make[2]: *** [help.txt] Error 2 make[2]: Leaving directory `/home/danjanies/poy4-read-only/src' make[1]: *** [depend] Error 2 make[1]: Leaving directory `/home/danjanies/poy4-read-only' make: *** [all] Error 2 have not changed mpich install on the cluster whats wrong? THANKS! Dan

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