<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="">Hi Carson,<div class=""><br class=""></div><div class="">Thanks for the feedback, I’ll look into the maker INSTALL file to ensure things are setup correctly.</div><div class=""><br class=""></div><div class="">Should I be looking into MPICH3 instead? I’m trying to run maker on a single node (~20 CPUs), rather than distribute it across our cluster. I assume that using MPICH3 changes the mpiexec / mpirun executable, but not the commands otherwise? I ask as I may have to configure this myself one day, so any tips appreciated. In the meantime your comments seem straightforward, will give it a shot.</div><div class=""><br class=""></div><div class="">All the best,</div><div class="">-Tim</div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On Apr 18, 2017, at 11:10 AM, Carson Holt <<a href="mailto:carsonhh@gmail.com" class="">carsonhh@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class="">
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" class=""><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">I agree that just using MPICH3 is the easiest solution. But to use OpenMPI you will need to export the environmental variables add the command line flags to mpiexec explained in the ../maker/INSTALL file.<div class=""><br class=""></div><div class="">#this must be doen exery time you run it</div><div class="">export LD_PRELOAD=/location/of/openmpi/lib/libmpi.so<br class=""><div class=""><br class=""></div><div class=""># -mca btl ^openib myust be on the command line</div><div class="">mpiexec -mca btl ^openib -n 20 maker</div><div class=""><br class=""></div><div class="">#alternatively add --mca btl vader,tcp,self --mca btl_tcp_if_include ib0 (use ib0 or whatever adapter interface exists on your cluster)</div><div class="">mpiexec --mca btl vader,tcp,self --mca btl_tcp_if_include ib0 -n 20 maker</div><div class=""><br class=""></div><div class="">—Carson</div><div class=""><br class=""><div class=""><blockquote type="cite" class=""><div class="">On Apr 17, 2017, at 9:35 AM, Tim Fallon <<a href="mailto:tfallon@mit.edu" class="">tfallon@mit.edu</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Hi there,<div class=""><br class=""></div><div class="">I’ve been troubleshooting the maker 3.0.0 beta plus MPI installation and configuration with our institute’s IT department. Despite a lot of tries and recompilations from scratch, we haven’t been able to get it to work (non-MPI maker works fine, albeit a bit slow). I’ve attached our most recent crash log when trying to run maker with MPI. Any tips? I’ve never used MPI before maker so not that familiar with troubleshooting it.</div><div class=""><br class=""></div><div class="">See below for my most recent contact with IT on it. I’ve also attached the most recent log file. We are trying to execute it through the LSF cluster submission tool, but I don’t think that is related to the problem. Any ideas?</div><div class=""><br class=""></div><div class="">"</div><div class=""><div style="margin-top: 0px; margin-bottom: 0px; font-family: Arial, Helvetica, sans-serif; font-size: 13px;" class="">I think one option is to try a build on a host without the full suite of cluster software. It may actually help, but if nothing else we can say that our problem exists with a (relatively) vanilla ubuntu linux host.<br class=""><br class="">Peter Macfarlane / WIBR IT<br class=""><br class=""><br class="">Description : Hi Peter,</div><div class=""><br class=""></div><div class="">Hoping to hear back from you on this. It does seem like we’ve exhausted the reasonable troubleshooting for this maker MPI execution, but maybe worth another shot before I ask the developers?</div><div class=""><br class=""></div><div class="">All the best,</div><div class="">-Tim</div><div class=""><br class=""><div class=""><blockquote class=""><div class="">On Apr 7, 2017, at 9:11 AM, Tim Fallon <<a href="mailto:tfallon@mit.edu" class="">tfallon@mit.edu</a>> wrote:</div><br class=""><div class="">Hi Peter,<div class=""><br class=""></div><div class="">I’ve tested with the following command:</div><div class="">bsub -o bsub_maker_with_mpi_log.txt "/nfs/apps/test/openmpi/bin/mpirun -n 8 /nfs/apps/test/maker/bin/maker”</div><div class=""><br class=""></div><div class="">Unfortunately it still seems to be giving errors and not running, with things like:</div><div class="">"“mca_base_component_repository_open: unable to open mca_patcher_overwrite: /nfs/apps/test/openmpi/lib/openmpi/mca_patcher_overwrite.so: undefined symbol: mca_patcher_base_patch_t_class (ignored)””</div><div class=""><br class=""></div><div class="">It also doesn’t work if I try to run it directly on Tak4.</div><div class=""><br class=""></div><div class="">I’ve attached the relevant error log file. Any more solutions?</div><div class=""><br class=""></div><div class="">All the best,</div><div class="">-Tim</div><div class=""><br class=""><div class=""><blockquote class=""><div class="">On Apr 5, 2017, at 3:50 PM, IT Systems Group <<a href="mailto:unix-help@wi.mit.edu" class="">unix-help@wi.mit.edu</a>> wrote:</div><br class=""><div class=""><div style="margin-top: 0px; margin-bottom: 0px; font-family: Arial, Helvetica, sans-serif; font-size: 13px;" class="">I tried rebuilding maker 3 with it's own also-built-from-source openmpi instance. So with that:<br class=""><br class="">- /nfs/apps/test/maker is now maker 3.00<br class="">- /nfs/apps/test/openmpi was used to make the aforementioned maker<br class=""><br class="">I think that all you'll need to do differently here is invoke the version of mpirun in /nfs/apps/test/openmpi/bin</div></div><div style="margin-top: 0px; margin-bottom: 0px; font-family: Arial, Helvetica, sans-serif; font-size: 13px;" class="">"</div></blockquote></div></div></div></blockquote></div></div></div><div class="">All the best,</div><div class="">-Tim</div><div class=""><br class=""><div class="">
<div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div style="letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div style="letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div style="letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div style="letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div style="letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div style="letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div style="letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div style="letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div style="font-family: Helvetica; font-style: normal; font-variant-ligatures: normal; font-variant-position: normal; font-variant-caps: normal; font-variant-numeric: normal; font-variant-alternates: normal; font-variant-east-asian: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-stroke-width: 0px; font-variant-ligatures: normal; font-variant-position: normal; font-variant-numeric: normal; font-variant-alternates: normal; font-variant-east-asian: normal; line-height: normal; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Timothy R. Fallon</div><div style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-stroke-width: 0px; font-variant-ligatures: normal; font-variant-position: normal; font-variant-numeric: normal; font-variant-alternates: normal; font-variant-east-asian: normal; line-height: normal; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">PhD candidate</div><div style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-stroke-width: 0px; font-variant-ligatures: normal; font-variant-position: normal; font-variant-numeric: normal; font-variant-alternates: normal; font-variant-east-asian: normal; line-height: normal; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Laboratory of Jing-Ke Weng</div><div style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-stroke-width: 0px; font-variant-ligatures: normal; font-variant-position: normal; font-variant-numeric: normal; font-variant-alternates: normal; font-variant-east-asian: normal; line-height: normal; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Department of Biology<br class="">MIT</div><div style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-stroke-width: 0px; font-variant-ligatures: normal; font-variant-position: normal; font-variant-numeric: normal; font-variant-alternates: normal; font-variant-east-asian: normal; line-height: normal; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><br class=""></div><div style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-stroke-width: 0px; font-variant-ligatures: normal; font-variant-position: normal; font-variant-numeric: normal; font-variant-alternates: normal; font-variant-east-asian: normal; line-height: normal; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><a href="mailto:tfallon@mit.edu" class="">tfallon@mit.edu</a></div></div></div></div></div></div></div></div></div></div></div>
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<br class=""></div><div class=""></div></div><span id="cid:8EECC5D3-8839-45DE-8F55-80193F6FB0F6@genetics.utah.edu" class=""><bsub_maker_with_mpi_log.txt></span><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div class=""></div></div>_______________________________________________<br class="">maker-devel mailing list<br class=""><a href="mailto:maker-devel@box290.bluehost.com" class="">maker-devel@box290.bluehost.com</a><br class=""><a href="http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org" class="">http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org</a><br class=""></div></blockquote></div><br class=""></div></div></div></div></blockquote></div><br class=""><div class="">
<div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div style="color: rgb(0, 0, 0); letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div style="color: rgb(0, 0, 0); letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div style="color: rgb(0, 0, 0); letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div style="color: rgb(0, 0, 0); letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div style="color: rgb(0, 0, 0); letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div style="color: rgb(0, 0, 0); letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div style="color: rgb(0, 0, 0); letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div style="color: rgb(0, 0, 0); letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div style="color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant-ligatures: normal; font-variant-position: normal; font-variant-caps: normal; font-variant-numeric: normal; font-variant-alternates: normal; font-variant-east-asian: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div style="color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-stroke-width: 0px; font-variant-ligatures: normal; font-variant-position: normal; font-variant-numeric: normal; font-variant-alternates: normal; font-variant-east-asian: normal; line-height: normal; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Timothy R. Fallon</div><div style="color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-stroke-width: 0px; font-variant-ligatures: normal; font-variant-position: normal; font-variant-numeric: normal; font-variant-alternates: normal; font-variant-east-asian: normal; line-height: normal; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">PhD candidate</div><div style="color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-stroke-width: 0px; font-variant-ligatures: normal; font-variant-position: normal; font-variant-numeric: normal; font-variant-alternates: normal; font-variant-east-asian: normal; line-height: normal; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Laboratory of Jing-Ke Weng</div><div style="color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-stroke-width: 0px; font-variant-ligatures: normal; font-variant-position: normal; font-variant-numeric: normal; font-variant-alternates: normal; font-variant-east-asian: normal; line-height: normal; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Department of Biology<br class="">MIT</div><div style="color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-stroke-width: 0px; font-variant-ligatures: normal; font-variant-position: normal; font-variant-numeric: normal; font-variant-alternates: normal; font-variant-east-asian: normal; line-height: normal; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><br class=""></div><div style="color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-stroke-width: 0px; font-variant-ligatures: normal; font-variant-position: normal; font-variant-numeric: normal; font-variant-alternates: normal; font-variant-east-asian: normal; line-height: normal; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><a href="mailto:tfallon@mit.edu" class="">tfallon@mit.edu</a></div></div></div></div></div></div></div></div></div></div></div>
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