<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">The parameters needed to get OpenMPI to work with MAKER are described in the …/maker/INSTALL file (specifically look at LD_PRELOAD and -mca btl ^openib) —> <br class=""><div><br class=""></div><div><div><font face="Courier" class="">!!IMPORTANT!!</font></div><div><font face="Courier" class="">MAKER is not compatible with MVAPICH2. Use OpenMPI or MPICH. If using MPICH, make</font></div><div><font face="Courier" class="">sure to enable shared libaries during installation (this is not the default). If</font></div><div><font face="Courier" class="">using OpenMPI, make sure to set LD_PRELOAD to the location of libmpi.so before</font></div><div><font face="Courier" class="">even trying to install MAKER. It must also be set before running MAKER (or any</font></div><div><font face="Courier" class="">program that uses OpenMPI's shared libraries), so it's best just to add it to</font></div><div><font face="Courier" class="">your ~/.bash_profile. (i.e. export LD_PRELOAD=/usr/local/openmpi/lib/libmpi.so).</font></div><div><font face="Courier" class=""><br class=""></font></div><div><font face="Courier" class=""><br class=""></font></div><div><font face="Courier" class="">1. Say yes to the 'configure for MPI' question when running 'perl Build.PL' in</font></div><div><font face="Courier" class=""> step 1 of the EASY INSTALL.</font></div><div><font face="Courier" class=""><br class=""></font></div><div><font face="Courier" class="">2. Give path to 'mpicc'. Note to make sure you do not give the path to 'mpicc'</font></div><div><font face="Courier" class=""> from another MPI flavor that might be installed on your system.</font></div><div><font face="Courier" class=""><br class=""></font></div><div><font face="Courier" class="">3. Give path to the folder containing 'mpi,h'. Note to make sure you do not</font></div><div><font face="Courier" class=""> give the path to a folder from another MPI flavor that might be installed</font></div><div><font face="Courier" class=""> on your system. Mixing MPI flavors for 'mpicc' and 'mpi.h' will cause</font></div><div><font face="Courier" class=""> failures. Make sure to read and confirm the auto-detected paths.</font></div><div><font face="Courier" class=""><br class=""></font></div><div><font face="Courier" class="">4. Finish installation according to steps 2-4 of the EASY INSTALL</font></div><div><font face="Courier" class=""><br class=""></font></div><div><font face="Courier" class=""> Note: For OpenMPI you may also want to set OMPI_MCA_mpi_warn_on_fork=0 in</font></div><div><font face="Courier" class=""> your ~/.bash_profile to turn off certain nonfatal warnings.</font></div><div><font face="Courier" class=""><br class=""></font></div><div><font face="Courier" class=""> Note: If jobs hang or freeze when using mpiexec under OpenMPI try adding</font></div><div><font face="Courier" class=""> the '-mca btl ^openib' flag to mpiexec command when running MAKER.</font></div><div><font face="Courier" class=""><br class=""></font></div><div><font face="Courier" class=""> Example: mpiexec -mca btl ^openib -n 20 maker</font></div></div><div><br class=""></div><div><br class=""></div><div><br class=""></div><div>Then to diable the forks warning, just add the parameter --mca mpi_warn_on_fork 0 to the mpiexec options as described in the warning.</div><div><br class=""></div><div>How to run with OpenMPi has also been covered extensively ibn the MAKER list archives and more detail can be found there —> <a href="https://groups.google.com/forum/#!searchin/maker-devel/openmpi|sort:date" class="">https://groups.google.com/forum/#!searchin/maker-devel/openmpi%7Csort:date</a></div><div><br class=""></div><div>Thanks,</div><div>Carson</div><div><br class=""></div><div><br class=""></div><div><br class=""><blockquote type="cite" class=""><div class="">On Nov 27, 2017, at 6:18 AM, HAI WANG <<a href="mailto:wanghai01@caas.cn" class="">wanghai01@caas.cn</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div class="Section1" style="page: Section1; font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;"><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Dear Professor Yandell,<o:p class=""></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">I am Hai Wang, a visiting scholar in Cornell University. I am sorry to bother you, but I really need your help. I am now using the maker pipeline to annotate a maize genome. The installation of maker, openmpi and other software should be OK since I’ve successfully run maker on your example data.<o:p class=""></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">But when I ran maker on my own maize genome, I always got the following error:<o:p class=""></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">A process has executed an operation involving a call to the<o:p class=""></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">"fork()" system call to create a child process. Open MPI is currently<o:p class=""></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">operating in a condition that could result in memory corruption or<o:p class=""></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">other system errors; your job may hang, crash, or produce silent<o:p class=""></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">data corruption. The use of fork() (or system() or other calls that<o:p class=""></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">create child processes) is strongly discouraged.<o:p class=""></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">The process that invoked fork was:<o:p class=""></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""> Local host: [[21269,1],0] (PID 12537)<o:p class=""></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">If you are *absolutely sure* that your application will successfully<o:p class=""></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">and correctly survive a call to fork(), you may disable this warning<o:p class=""></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">by setting the mpi_warn_on_fork MCA parameter to 0.<o:p class=""></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">--------------------------------------------------------------------------<o:p class=""></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">--------------------------------------------------------------------------<o:p class=""></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">mpiexec noticed that process rank 32 with PID 0 on node fat1 exited on signal 11 (Segmentation fault).<o:p class=""></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">--------------------------------------------------------------------------<o:p class=""></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Could you please help me with this issue? Or is there a way that I can resume this job when it stops? Thank you very much!<o:p class=""></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Best,<o:p class=""></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Hai Wang<o:p class=""></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div></div><span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">_______________________________________________</span><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">maker-devel mailing list</span><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><a href="mailto:maker-devel@box290.bluehost.com" style="color: purple; text-decoration: underline; font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;" class="">maker-devel@box290.bluehost.com</a><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><a href="http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org" style="color: purple; text-decoration: underline; font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;" class="">http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org</a></div></blockquote></div><br class=""></body></html>