<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div class="">Hi Jackie,</div><div class=""><br class=""></div>From the INSTALL file included with MAKER —><div class=""><br class=""></div><div class=""><font face="Courier" class=""> Note: For OpenMPI you may also want to set OMPI_MCA_mpi_warn_on_fork=0 in<br class=""> your ~/.bash_profile to turn off certain nonfatal warnings.<br class=""><br class=""> Note: If jobs hang or freeze when using mpiexec under OpenMPI try adding<br class=""> the '-mca btl ^openib' flag to mpiexec command when running MAKER.<br class=""><br class=""> Example: mpiexec -mca btl ^openib -n 20 maker</font></div><div class=""><br class=""></div><div class=""><br class=""></div><div class="">Also the following —></div><div class=""><br class=""></div><blockquote style="margin: 0 0 0 40px; border: none; padding: 0px;" class=""><div class=""><font face="Courier" class="">If using OpenMPI, make sure to set LD_PRELOAD to the location of libmpi.so before</font></div><div class=""><font face="Courier" class="">even trying to install MAKER. It must also be set before running MAKER (or any</font></div><div class=""><font face="Courier" class="">program that uses OpenMPI's shared libraries), so it's best just to add it to</font></div><div class=""><font face="Courier" class="">your ~/.bash_profile. (i.e. export LD_PRELOAD=/usr/local/openmpi/lib/libmpi.so).</font></div></blockquote><div class=""><br class=""></div><div class=""><br class=""></div><div class="">The first one is the most likely.</div><div class=""><br class=""></div><div class="">Thanks,</div><div class="">Carson</div><div class=""><br class=""></div><div class=""><br class=""></div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On Mar 28, 2016, at 8:38 AM, Atkins, Jacqueline (NIH/NIAID) [C] <<a href="mailto:jacqueline.atkins@nih.gov" class="">jacqueline.atkins@nih.gov</a>> wrote:</div><br class="Apple-interchange-newline"><div class="">
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<div style="font-size: 14px;" class="">Hello,</div>
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<div style="font-size: 14px;" class="">I have recently installed Maker on RHEL 7/ Perl-5.16.3. When I attempt to execute, I get the following error</div>
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<div class="">$ <span style="font-family: Menlo;" class="">mpiexec -n 4 maker -help</span></div>
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<div class=""><div style="margin: 0px; font-family: Menlo;" class="">An MPI process has executed an operation involving a call to the</div><div style="margin: 0px; font-family: Menlo;" class="">"fork()" system call to create a child process. Open MPI is currently</div><div style="margin: 0px; font-family: Menlo;" class="">operating in a condition that could result in memory corruption or</div><div style="margin: 0px; font-family: Menlo;" class="">other system errors; your MPI job may hang, crash, or produce silent</div><div style="margin: 0px; font-family: Menlo;" class="">data corruption. The use of fork() (or system() or other calls that</div><div style="margin: 0px; font-family: Menlo;" class="">create child processes) is strongly discouraged. </div><div style="margin: 0px; font-family: Menlo; min-height: 22px;" class=""><br class="">
</div><div style="margin: 0px; font-family: Menlo;" class="">The process that invoked fork was:</div><div style="margin: 0px; font-family: Menlo; min-height: 22px;" class=""><br class="">
</div><div style="margin: 0px; font-family: Menlo;" class=""> Local host: submit (PID 316)</div><div style="margin: 0px; font-family: Menlo;" class=""> MPI_COMM_WORLD rank: 2</div><div style="margin: 0px; font-family: Menlo; min-height: 22px;" class=""><br class="">
</div><div style="margin: 0px; font-family: Menlo;" class="">If you are *absolutely sure* that your application will successfully</div><div style="margin: 0px; font-family: Menlo;" class="">and correctly survive a call to fork(), you may disable this warning</div><div style="margin: 0px; font-family: Menlo;" class="">by setting the mpi_warn_on_fork MCA parameter to 0.</div><div style="margin: 0px; font-family: Menlo;" class="">--------------------------------------------------------------------------</div><div style="margin: 0px; font-family: Menlo;" class="">[submit:122878] 3 more processes have sent help message help-mpi-runtime.txt / mpi_init:warn-fork</div><div style="margin: 0px; font-family: Menlo;" class="">[submit:122878] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages</div><div style="margin: 0px; font-family: Menlo;" class="">[submit bin]$ mpiexec --version</div><div style="margin: 0px; font-family: Menlo;" class="">mpiexec (OpenRTE) 1.8.4</div>
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<div class="">I have a previous version of Maker installed that is using OpenMPI 1.3.3 and it is working fine. I was wondering if you think this might be related to the version of OpenMPI?</div>
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<div class="">Thank you in advance.</div>
<div class="">Jackie</div>
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