<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 Ann,</div><div class=""><br class=""></div><div class="">Build.PL just configures (the status message only shows me your configuration choices). You still have to run './Build install’. Your error shows that you configured maker for MPI but never ran the install step successfully.</div><div class=""><br class=""></div><div class="">You should get something like this —></div><div class=""><br class=""></div><div class=""><font face="Courier" class="">$ ./Build install<br class="">Installing MAKER...<br class="">Configuring MAKER with MPI support<br class="">Installing maker/2.31.8/src/../perl/lib/Parallel/Application/MPI.pm<br class="">Installing maker/2.31.8/src/../perl/lib/auto/Parallel/Application/MPI/MPI.so<br class="">Installing maker/2.31.8/src/../perl/lib/auto/Parallel/Application/MPI/MPI.inl<br class="">cp blib/config-x86_64-linux-thread-multi-5.010001 maker/2.31.8/src/../perl/config-x86_64-linux-thread-multi-5.010001</font></div><div class=""><br class=""></div><div class=""><br class=""></div><div class="">Thanks,</div><div class="">Carson</div><div class=""><br class=""></div><div class=""><br class=""></div><br class=""><div><blockquote type="cite" class=""><div class="">On Jun 11, 2015, at 3:44 PM, Ann Danowitz <<a href="mailto:adanowitz8@gmail.com" class="">adanowitz8@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class="">Hello Yandell maker gurus,<div class=""><br class=""></div><div class="">Installed Maker 2.31 with MPICH2 .</div><div class="">No errors with Build.PL and Build install </div><div class=""><div class="">==============================================================================</div><div class="">STATUS MAKER v2.31.8</div><div class="">==============================================================================</div><div class="">PERL Dependencies:<span class="" style="white-space:pre"> </span>VERIFIED</div><div class="">External Programs:<span class="" style="white-space:pre"> </span>VERIFIED</div><div class="">External C Libraries:<span class="" style="white-space:pre"> </span>VERIFIED</div><div class="">MPI SUPPORT:<span class="" style="white-space:pre"> </span>ENABLED</div><div class="">MWAS Web Interface:<span class="" style="white-space:pre"> </span>DISABLED</div><div class="">MAKER PACKAGE:<span class="" style="white-space:pre"> </span>CONFIGURATION OK</div></div><div class=""><br class=""></div><div class="">but with the following command, maker fails:</div><div class=""><br class=""></div><div class="">dcopetti@bam:/opt/bam_processing/Dario/MAKER_mpi[4:21pm]> mpiexec -n 20 /opt/maker/bin/maker maker_opts_wg_bam_mpi.ctl maker_bopts_wg_bam_mpi.ctl maker_exe_wg_bam_mpi.ctl<br class=""></div><div class=""><br class=""></div><div class=""><div class=""> at /opt/maker/bin/../perl/lib/Parallel/Application/MPI.pm line 236.</div><div class="">--> rank=NA, hostname=<a href="http://bam.genome.arizona.edu/" class="">bam.genome.arizona.edu</a></div><div class=""> ...propagated at /usr/local/share/perl5/Inline/C.pm line 772.</div><div class="">--> rank=NA, hostname=<a href="http://bam.genome.arizona.edu/" class="">bam.genome.arizona.edu</a></div><div class=""> at /opt/maker/bin/../perl/lib/Parallel/Application/MPI.pm line 256.</div><div class=""> Parallel::Application::MPI::_bind("/usr/lib64/openmpi/bin/mpicc", "/usr/include", "/opt/maker/bin/../perl", "") called at /opt/maker/bin/../perl/lib/Parallel/Application/MPI.pm line 213</div><div class=""> Parallel::Application::MPI::_load() called at /opt/maker/bin/../perl/lib/Parallel/Application/MPI.pm line 74</div><div class=""> Parallel::Application::MPI::MPI_Init() called at /opt/maker/bin/maker line 279</div><div class=""><br class=""></div><div class="">{line 279 stat = MPI_Init(&PL_origargc, &PL_origargv);}</div><div class=""><br class=""></div><div class="">make: *** No targets specified and no makefile found. Stop.</div></div><div class=""><br class=""></div><div class=""><div class="">A problem was encountered while attempting to compile and install your Inline<br class=""></div><div class="">C code. The command that failed was:</div><div class=""> make > out.make 2>&1</div></div><div class=""><br class=""></div><div class=""><div class="">[root@bam ~]# more /opt/maker/perl/build/Parallel/Application/MPI/out.make_install</div><div class="">Makefile:123: warning: NUL character seen; rest of line ignored</div><div class="">Makefile:123: *** missing separator. Stop.</div><div class=""><br class=""></div><div class="">also from out.make in the same directory:</div><div class="">make: *** [MPI.c] mv: cannot stat `MPI.xsc': No such file or directory</div><div class="">make: *** [MPI.c] Error 1</div><div class=""> or directory</div><div class="">make: *** [MPI.c] Error 1</div></div><div class=""><br class=""></div><div class="">What values are not getting passed to MPI.pm?</div><div class=""><br class=""></div><div class="">Many thanks for any help!</div></div>
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