<html><head><meta http-equiv="Content-Type" content="text/html charset=us-ascii"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Stampede only has MVAPICH2. It does not have OpenMPI (even though it has been requested several times). OpenFabrics libraries (used by MVAPICH2) have a known issue that restricts programs from making system calls while running under MPI. A system call is when one program launches another (i.e. MAKER launching BLAST). For this reason MAKER does not work with MVAPICH2. It only works with OpenMPI.<div class=""><br class=""></div><div class="">You can still get it to work on MVAPICH2, but only on a single node. If you request more than one node then it will fail. The solution would be for TACC to install OpenMPI as an option on Stampede (like they have on Lonestar), but until that happens you can only run MAKER on a single node.</div><div class=""><br class=""></div><div class="">Thanks,</div><div class="">Carson</div><div class=""><br class=""></div><div class=""><div class=""><div class=""><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On Jan 22, 2015, at 10:51 PM, Won C Yim <<a href="mailto:wyim@unr.edu" class="">wyim@unr.edu</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div id="bloop_customfont" style="font-family: Helvetica, Arial; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: 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; margin: 0px;" class="">Dear anyone whom may it concern,</div><div id="bloop_customfont" style="font-family: Helvetica, Arial; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: 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; margin: 0px;" class=""><br class=""></div><div id="bloop_customfont" style="font-family: Helvetica, Arial; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: 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; margin: 0px;" class="">Hi!</div><div id="bloop_customfont" style="font-family: Helvetica, Arial; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: 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; margin: 0px;" class=""><br class=""></div><div id="bloop_customfont" style="font-family: Helvetica, Arial; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: 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; margin: 0px;" class="">My name is Won Cheol Yim in University of Nevada, Reno.</div><div id="bloop_customfont" style="font-family: Helvetica, Arial; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: 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; margin: 0px;" class=""><br class=""></div><div id="bloop_customfont" style="font-family: Helvetica, Arial; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: 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; margin: 0px;" class="">I try to run MAKER on TACC Stampede.</div><div id="bloop_customfont" style="font-family: Helvetica, Arial; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: 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; margin: 0px;" class=""><br class=""></div><div id="bloop_customfont" style="font-family: Helvetica, Arial; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: 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; margin: 0px;" class="">It looks everything installed properly.</div><div id="bloop_customfont" style="font-family: Helvetica, Arial; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: 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; margin: 0px;" class=""><br class=""></div><div id="bloop_customfont" style="font-family: Helvetica, Arial; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: 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; margin: 0px;" class=""><div id="bloop_customfont" style="margin: 0px;" class="">==============================================================================</div><div id="bloop_customfont" style="margin: 0px;" class="">STATUS MAKER v2.31.8</div><div id="bloop_customfont" style="margin: 0px;" class="">==============================================================================</div><div id="bloop_customfont" style="margin: 0px;" class="">PERL Dependencies:<span class="Apple-tab-span" style="white-space: pre;">
</span>VERIFIED</div><div id="bloop_customfont" style="margin: 0px;" class="">External Programs:<span class="Apple-tab-span" style="white-space: pre;">
</span>VERIFIED</div><div id="bloop_customfont" style="margin: 0px;" class="">External C Libraries:<span class="Apple-tab-span" style="white-space: pre;">
</span>VERIFIED</div><div id="bloop_customfont" style="margin: 0px;" class="">MPI SUPPORT:<span class="Apple-tab-span" style="white-space: pre;">
</span>ENABLED</div><div id="bloop_customfont" style="margin: 0px;" class="">MWAS Web Interface:<span class="Apple-tab-span" style="white-space: pre;">
</span>DISABLED</div><div id="bloop_customfont" style="margin: 0px;" class="">MAKER PACKAGE:<span class="Apple-tab-span" style="white-space: pre;">
</span>CONFIGURATION OK</div><div id="bloop_customfont" style="margin: 0px;" class=""><br class=""></div><div id="bloop_customfont" style="margin: 0px;" class="">And I installed Perl 5.18.4 with threads option.</div><div id="bloop_customfont" style="margin: 0px;" class=""><br class=""></div><div id="bloop_customfont" style="margin: 0px;" class="">But I try to run it with MPI, it generated error.</div><div id="bloop_customfont" style="margin: 0px;" class=""><br class=""></div><div id="bloop_customfont" style="margin: 0px;" class="">I assumed this problem came from ibrun in Stampede.</div><div id="bloop_customfont" style="margin: 0px;" class=""><br class=""></div><div id="bloop_customfont" style="margin: 0px;" class="">Is there anyway to run it on Stampede?</div><div id="bloop_customfont" style="margin: 0px;" class=""><br class=""></div><div id="bloop_customfont" style="margin: 0px;" class="">Here is my log.</div><div id="bloop_customfont" style="margin: 0px;" class=""><br class=""></div><div id="bloop_customfont" style="margin: 0px;" class=""><div id="bloop_customfont" style="margin: 0px;" class="">TACC: Starting up job</div><div id="bloop_customfont" style="margin: 0px;" class="">TACC: Setting up parallel environment for MVAPICH ssh-based mpirun.</div><div id="bloop_customfont" style="margin: 0px;" class="">cat: /home1/02908/wyim/.sge/job..hostlist.kUm5vXw9: No such file or directory</div><div id="bloop_customfont" style="margin: 0px;" class="">sort: open failed: /home1/02908/wyim/.sge/job..hostlist.kUm5vXw9: No such file or directory</div><div id="bloop_customfont" style="margin: 0px;" class="">TACC: Setup complete. Running job script.</div><div id="bloop_customfont" style="margin: 0px;" class="">TACC: starting parallel tasks...</div><div id="bloop_customfont" style="margin: 0px;" class="">[c404-703.stampede.tacc.utexas.edu:mpirun_rsh][read_hostfile] Can't open hostfile `/home1/02908/wyim/.sge/job..hostlist.kUm5vXw9': (2)</div><div id="bloop_customfont" style="margin: 0px;" class="">TACC: MPI job exited with code: 1</div><div id="bloop_customfont" style="margin: 0px;" class="">TACC: Shutting down parallel environment.</div><div id="bloop_customfont" style="margin: 0px;" class="">TACC: Shutdown complete. Exiting.</div></div></div><div id="bloop_customfont" style="font-family: Helvetica, Arial; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: 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; margin: 0px;" class=""><br class=""></div><div id="bloop_customfont" style="font-family: Helvetica, Arial; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: 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; margin: 0px;" class=""><br class=""></div><div id="bloop_customfont" style="font-family: Helvetica, Arial; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: 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; margin: 0px;" class="">Regards,</div><div id="bloop_customfont" style="font-family: Helvetica, Arial; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: 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; margin: 0px;" class=""><br class=""></div><div id="bloop_customfont" style="font-family: Helvetica, Arial; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: 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; margin: 0px;" class="">Won</div><div id="bloop_sign_1421991416237999872" class="bloop_sign" style="font-family: Helvetica, Arial; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: 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;"><div style="font-family: helvetica, arial; font-size: 13px;" class="">-- <br class="">Yim, Won Cheol<br class="">Sent with Airmail</div></div></div></blockquote></div><br class=""></div></div></div></div></body></html>