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<div>Just default, /work/02045/jiao/modules/Maker-GMOD/maker-dev/exe/mpich2/bin/mpicc and /work/02045/jiao/modules/Maker-GMOD/maker-dev/exe/mpich2/include</div>
<div>
<div>
<div>-- </div>
<div><span class="Apple-style-span" style="font-size: 13px; font-family: Calibri; ">Dian (Oscar) Jiao, Ph.D.,<br>
Research Associate, Life Sciences Computing Group<br>
Texas Advanced Computing Center<br>
University of Texas at Austin<br>
jiao@tacc.utexas.edu | (832) 303-1166</span></div>
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<span style="font-weight:bold">From: </span>Carson Holt <<a href="mailto:carsonhh@gmail.com">carsonhh@gmail.com</a>><br>
<span style="font-weight:bold">Date: </span>Friday, October 5, 2012 3:03 PM<br>
<span style="font-weight:bold">To: </span>Oscar Jiao <<a href="mailto:jiao@tacc.utexas.edu">jiao@tacc.utexas.edu</a>>, "<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>" <<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>><br>
<span style="font-weight:bold">Subject: </span>Re: [maker-devel] maker mpi failed<br>
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<div>What were you answers to the mpicc and mpi.h questions during setup?</div>
<div><br>
</div>
<div>--Carson</div>
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<span style="font-weight:bold">From: </span>"Dian \"Oscar\" Jiao" <<a href="mailto:jiao@tacc.utexas.edu">jiao@tacc.utexas.edu</a>><br>
<span style="font-weight:bold">Date: </span>Friday, 5 October, 2012 3:55 PM<br>
<span style="font-weight:bold">To: </span>Carson Holt <<a href="mailto:carsonhh@gmail.com">carsonhh@gmail.com</a>>, "<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>" <<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>><br>
<span style="font-weight:bold">Subject: </span>Re: [maker-devel] maker mpi failed<br>
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<div>I got problem installing the dev version Maker. Here is what I did:</div>
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</div>
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<div>./Build mpich2</div>
<div>perl Build.PL</div>
<div>
<div>(yes to MPI)</div>
<div>./Build clean</div>
</div>
<div>./Build install</div>
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<div><br>
</div>
<div>The install fails while configuring Maker with MPI support:</div>
<div>
<div>Had problems bootstrapping Inline module 'Parallel::Application::MPI'</div>
<div><br>
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<div>Can't load '/work/02045/jiao/modules/Maker-GMOD/maker-dev/src/blib/lib/auto/Parallel/Application/MPI/MPI.so' for module Parallel::Application::MPI: libifport.so.5: cannot open shared object file: No such file or directory at /work/02045/jiao/localperl/lib/5.16.1/x86_64-linux-thread-multi/DynaLoader.pm
line 190.</div>
<div> at /work/02045/jiao/localperl/add-on/lib/site_perl/5.16.1/Inline.pm line 536.</div>
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<div> at /work/02045/jiao/modules/Maker-GMOD/maker-dev/src/lib/Parallel/Application/MPI.pm line 223.</div>
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<div><br>
</div>
<div>** If you are running using OpenMPI, you may have to preload object files</div>
<div>** for shared libraries to work. For bash, try executing a command</div>
<div>** similar to the following with the appropriate file location.</div>
<div>** Example --> export LD_PRELOAD=.../openmpi/lib/libmpi.so</div>
<div>** Please do this before trying to run MAKER again!!</div>
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<div><br>
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<div>Something wrong with my DynaLoader/Inline modules? Version 2.26 installed ok. What is the difference between 2.26 and the development version?</div>
<div><br>
</div>
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<div>
<div>-- </div>
<div><span class="Apple-style-span" style="font-size: 13px; font-family: Calibri; ">Dian (Oscar) Jiao, Ph.D.,</span><span class="Apple-style-span" style="font-size: 13px; font-family: Calibri; "><br>
</span><span class="Apple-style-span" style="font-size: 13px; font-family: Calibri; ">Research Associate, Life Sciences Computing Group</span><span class="Apple-style-span" style="font-size: 13px; font-family: Calibri; "><br>
</span><span class="Apple-style-span" style="font-size: 13px; font-family: Calibri; ">Texas Advanced Computing Center</span><span class="Apple-style-span" style="font-size: 13px; font-family: Calibri; "><br>
</span><span class="Apple-style-span" style="font-size: 13px; font-family: Calibri; ">University of Texas at Austin</span><span class="Apple-style-span" style="font-size: 13px; font-family: Calibri; "><br>
</span><span class="Apple-style-span" style="font-size: 13px; font-family: Calibri; "><a href="mailto:jiao@tacc.utexas.edu">jiao@tacc.utexas.edu</a> | (832) 303-1166</span></div>
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<span style="font-weight:bold">From: </span>Carson Holt <<a href="mailto:carsonhh@gmail.com">carsonhh@gmail.com</a>><br>
<span style="font-weight:bold">Date: </span>Friday, October 5, 2012 1:19 PM<br>
<span style="font-weight:bold">To: </span>Oscar Jiao <<a href="mailto:jiao@tacc.utexas.edu">jiao@tacc.utexas.edu</a>>, "<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>" <<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>><br>
<span style="font-weight:bold">Subject: </span>Re: [maker-devel] maker mpi failed<br>
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<div>Could you try the development version anyways with MPI using the same procedure and send me the results as you did with 2.26?</div>
<div><br>
</div>
<div>Thanks,</div>
<div>Carson</div>
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<span style="font-weight:bold">From: </span>"Dian \"Oscar\" Jiao" <<a href="mailto:jiao@tacc.utexas.edu">jiao@tacc.utexas.edu</a>><br>
<span style="font-weight:bold">Date: </span>Friday, 5 October, 2012 2:16 PM<br>
<span style="font-weight:bold">To: </span>Carson Holt <<a href="mailto:carsonhh@gmail.com">carsonhh@gmail.com</a>>, "<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>" <<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>><br>
<span style="font-weight:bold">Subject: </span>Re: [maker-devel] maker mpi failed<br>
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<div>See the attached files. The command I used "/work/02045/jiao/modules/Maker-GMOD/maker2.26/exe/mpich2/bin/mpiexec -n 12 /work/02045/jiao/modules/Maker-GMOD/maker2.26/bin/maker -debug maker_exe.ctl maker_opts.ctl maker_bopts.ctl 2> mpich-maker-debug.log"</div>
<div><br>
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<div>I am still using Maker 2.26. These problems I had earlier with AnyDBM_File were resolved (manually), so I did not install the development version.</div>
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<div>~Oscar</div>
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<span style="font-weight:bold">From: </span>Carson Holt <<a href="mailto:carsonhh@gmail.com">carsonhh@gmail.com</a>><br>
<span style="font-weight:bold">Date: </span>Friday, October 5, 2012 11:05 AM<br>
<span style="font-weight:bold">To: </span>Oscar Jiao <<a href="mailto:jiao@tacc.utexas.edu">jiao@tacc.utexas.edu</a>>, "<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>" <<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>><br>
<span style="font-weight:bold">Subject: </span>Re: [maker-devel] maker mpi failed<br>
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<div>Are you using the subversion version of MAKER I sent?</div>
<div><br>
</div>
<div>If so send me the following. Run under MPI with the --debug flag set on maker. When running, supply the full path to both the maker and mpiexec executables. Capture the STDERR to a file.</div>
<div><br>
</div>
<div>Send me that STDERR file together with the maker_opts.ctl file you are using.</div>
<div><br>
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<div>Thanks,</div>
<div>Carson</div>
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<span style="font-weight:bold">From: </span>"Dian \"Oscar\" Jiao" <<a href="mailto:jiao@tacc.utexas.edu">jiao@tacc.utexas.edu</a>><br>
<span style="font-weight:bold">Date: </span>Friday, 5 October, 2012 1:06 AM<br>
<span style="font-weight:bold">To: </span>Carson Holt <<a href="mailto:carsonhh@gmail.com">carsonhh@gmail.com</a>>, "<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>" <<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>><br>
<span style="font-weight:bold">Subject: </span>Re: [maker-devel] maker mpi failed<br>
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<div>I followed your instructions to compile Maker with MPICH2 (the one comes with Maker). But when I run maker with mpi, it terminates with the message:</div>
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<p style="color: rgb(0, 0, 0); font-family: arial, sans-serif; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255); ">
STATUS: Parsing control files... <br>
STATUS: Processing and indexing input FASTA files... <br>
=========================================================================== ========== <br>
</p>
<p style="color: rgb(0, 0, 0); font-family: arial, sans-serif; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255); ">
= BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES <br>
= EXIT CODE: 11 <br>
= CLEANING UP REMAINING PROCESSES <br>
= YOU CAN IGNORE THE BELOW CLEANUP MESSAGES <br>
=========================================================================== ========== <br>
</p>
<p style="color: rgb(0, 0, 0); font-family: arial, sans-serif; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255); ">
APPLICATION TERMINATED WITH THE EXIT STRING: Segmentation fault (signal 11) </p>
<p style="color: rgb(0, 0, 0); font-family: arial, sans-serif; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255); ">
The serial version of Maker still works. I tried to install MPICH2 manually outside maker and got the same error.</p>
</div>
<div>
<div>
<div>-- </div>
<div><span class="Apple-style-span" style="font-size: 13px; font-family: Calibri; ">Dian (Oscar) Jiao, Ph.D.,</span><span class="Apple-style-span" style="font-size: 13px; font-family: Calibri; "><br>
</span><span class="Apple-style-span" style="font-size: 13px; font-family: Calibri; ">Research Associate, Life Sciences Computing Group</span><span class="Apple-style-span" style="font-size: 13px; font-family: Calibri; "><br>
</span><span class="Apple-style-span" style="font-size: 13px; font-family: Calibri; ">Texas Advanced Computing Center</span><span class="Apple-style-span" style="font-size: 13px; font-family: Calibri; "><br>
</span><span class="Apple-style-span" style="font-size: 13px; font-family: Calibri; ">University of Texas at Austin</span><span class="Apple-style-span" style="font-size: 13px; font-family: Calibri; "><br>
</span><span class="Apple-style-span" style="font-size: 13px; font-family: Calibri; "><a href="mailto:jiao@tacc.utexas.edu">jiao@tacc.utexas.edu</a> | (832) 303-1166</span></div>
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<span style="font-weight:bold">From: </span>Carson Holt <<a href="mailto:carsonhh@gmail.com">carsonhh@gmail.com</a>><br>
<span style="font-weight:bold">Date: </span>Thursday, October 4, 2012 3:53 PM<br>
<span style="font-weight:bold">To: </span>Oscar Jiao <<a href="mailto:jiao@tacc.utexas.edu">jiao@tacc.utexas.edu</a>>, "<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>" <<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>><br>
<span style="font-weight:bold">Subject: </span>Re: [maker-devel] maker mpi failed<br>
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<div><br>
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<div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; color: rgb(0, 0, 0); font-size: 14px; font-family: Calibri, sans-serif; ">
<div>You either tried to run with the -dsindex option before the log file existed or you tried to launch via MPI when not compiled for MPI or not compiled correctly. It's as if you called MAKER serially multiple times in a row which you can do, but if you
start too many before one of them gets a chance to get the log file started a race condition exists.</div>
<div><br>
</div>
<div>Which MPI flavor are you using? MVAPICH2 won't work with MAKER, MPICH2 will, and OpenMPI may or may not (non-robust shared library behavior).</div>
<div><br>
</div>
<div>You may have to reinstall MPICH2.</div>
<div><br>
</div>
<div>MAKER can try and do this for you using necessary flags to make it easier</div>
<div>To do this --></div>
<div>cd ./maker/src</div>
<div>./Build mpich2</div>
<div><br>
</div>
<div>Then reinstall maker</div>
<div>
<div>cd ./maker/src</div>
<div>perl Build.PL</div>
<div><say yes to mpi question></div>
<div>./Build clean</div>
</div>
<div>./Build install</div>
<div><br>
</div>
<div>Then use this executable to launch --> ./maker/exe/mpich2/bin/mpiexec</div>
<div><br>
</div>
<div>Note you cannot use other launchers. You have to use the one you compiled with.</div>
<div><br>
</div>
<div>--Carson</div>
<div><br>
</div>
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<span style="font-weight:bold">From: </span>"Dian \"Oscar\" Jiao" <<a href="mailto:jiao@tacc.utexas.edu">jiao@tacc.utexas.edu</a>><br>
<span style="font-weight:bold">Date: </span>Thursday, 4 October, 2012 4:42 PM<br>
<span style="font-weight:bold">To: </span>"<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>" <<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>><br>
<span style="font-weight:bold">Subject: </span>[maker-devel] maker mpi failed<br>
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<div><br>
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<div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">
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<div style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif; font-size: 14px; ">
Hi, I was trying to run maker 2.26. It was compiled with MPI. The non-mpi executable works just fine. But I got the error below while running mpirun –n maker ……</div>
<div style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif; font-size: 14px; ">
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</div>
<div style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif; font-size: 14px; ">
What is this Iterator::Fasta::skip_file? Any idea what is going on here?</div>
<div style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif; font-size: 14px; ">
<br>
</div>
<div style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif; font-size: 14px; ">
Oscar</div>
<div style="font-family: Calibri, sans-serif; font-size: 14px; ">
<div style="color: rgb(0, 0, 0); "><br>
</div>
<div style="color: rgb(0, 0, 0); ">STATUS: Processing and indexing input FASTA files...</div>
<div style="color: rgb(0, 0, 0); ">STATUS: Setting up database for any GFF3 input...</div>
<div style="color: rgb(0, 0, 0); ">A data structure will be created for you at:</div>
<div style="color: rgb(0, 0, 0); ">/work/02045/jiao/modules/Maker-GMOD/maker2.26/data/dpp_contig.maker.output/dpp_contig_datastore</div>
<div style="color: rgb(0, 0, 0); "><br>
</div>
<div style="color: rgb(0, 0, 0); ">To access files for individual sequences use the datastore index:</div>
<div style="color: rgb(0, 0, 0); ">/work/02045/jiao/modules/Maker-GMOD/maker2.26/data/dpp_contig.maker.output/dpp_contig_master_datastore_index.log</div>
<div style="color: rgb(0, 0, 0); "><br>
</div>
<div><font class="Apple-style-span" color="#ff0000">ERROR: Log file does not exist in Iterator::Fasta::skip_file</font></div>
<div style="color: rgb(0, 0, 0); ">MPI process (rank: 8) terminated unexpectedly on c341-213.ls4.tacc.utexas.edu</div>
<div style="color: rgb(0, 0, 0); ">Exit code -5 signaled from c341-213</div>
</div>
<div style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif; font-size: 14px; ">
<br>
</div>
</div>
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</div>
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