<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="">MAKER does not work with mvapich2. You must use either OpenMPI or MPICH2.<div class=""><br class=""></div><div class="">The following is from the INSTALL instructions that come with MAKER —></div><div class=""><br class=""></div><div class=""><span class="" style="color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif; font-size: 13px; background-color: rgb(255, 255, 255);">If using OpenMPI, make sure to set LD_PRELOAD to the location of libmpi.so before even trying to install MAKER. </span><b class="" style="color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif; font-size: 13px;">It must also be set before running MAKER</b><span class="" style="color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif; font-size: 13px; background-color: rgb(255, 255, 255);"> (or any program that uses OpenMPI's shared libraries), so it's best just to add it to your ~/.bash_profile. (i.e. export LD_PRELOAD=/</span><wbr class="" style="color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif; font-size: 13px;"><span class="" style="color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif; font-size: 13px; background-color: rgb(255, 255, 255);">location/of/openmpi/lib/</span><wbr class="" style="color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif; font-size: 13px;"><span class="" style="color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif; font-size: 13px; background-color: rgb(255, 255, 255);">libmpi.so).</span><br class="" style="color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif; font-size: 13px;"><br class="" style="color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif; font-size: 13px;"><br class="" style="color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif; font-size: 13px;"><span class="" style="color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif; font-size: 13px; background-color: rgb(255, 255, 255);">1. Say yes to the 'configure for MPI' question when running 'perl Build.PL’ in step 1 of the EASY INSTALL.</span><br class="" style="color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif; font-size: 13px;"><br class="" style="color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif; font-size: 13px;"><span class="" style="color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif; font-size: 13px; background-color: rgb(255, 255, 255);">2. Give path to 'mpicc'. Note to make sure you do not give the path to ‘mpicc' from another MPI flavor that might be installed on your system.</span><br class="" style="color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif; font-size: 13px;"><br class="" style="color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif; font-size: 13px;"><span class="" style="color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif; font-size: 13px; background-color: rgb(255, 255, 255);">3. Give path to the folder containing 'mpi,h'. Note to make sure you do not give the path to a folder from another MPI flavor that might be installed on your system. Mixing MPI flavors for 'mpicc' and 'mpi.h' will cause failures. Make sure to read and confirm the auto-detected paths.</span><br class="" style="color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif; font-size: 13px;"><br class="" style="color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif; font-size: 13px;"><span class="" style="color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif; font-size: 13px; background-color: rgb(255, 255, 255);">4. Finish installation according to steps 2-4 of the EASY INSTALL</span><br class="" style="color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif; font-size: 13px;"><br class="" style="color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif; font-size: 13px;"><span class="" style="color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif; font-size: 13px; background-color: rgb(255, 255, 255);">Note: For OpenMPI you may also want to set OMPI_MCA_mpi_warn_on_fork=0 in your ~/.bash_profile to turn off certain nonfatal warnings.</span><br class="" style="color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif; font-size: 13px;"><br class="" style="color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif; font-size: 13px;"><span class="" style="color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif; font-size: 13px; background-color: rgb(255, 255, 255);">Note: If jobs hang or freeze when using mpiexec under OpenMPI try adding the '-mca btl ^openib' flag to mpiexec command when running MAKER.</span><br class="" style="color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif; font-size: 13px;"><br class="" style="color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif; font-size: 13px;"><span class="" style="color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif; font-size: 13px; background-color: rgb(255, 255, 255);"> Example: mpiexec -mca btl ^openib -n 20 maker</span></div><div class=""><span class="" style="color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif; font-size: 13px; background-color: rgb(255, 255, 255);"><br class=""></span></div><div class=""><span class="" style="color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif; font-size: 13px; background-color: rgb(255, 255, 255);">Thanks,</span></div><div class=""><span class="" style="color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif; font-size: 13px; background-color: rgb(255, 255, 255);">Carson</span></div><div class=""><span class="" style="color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif; font-size: 13px; background-color: rgb(255, 255, 255);"><br class=""></span></div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On Dec 17, 2015, at 11:03 AM, Hua Zhong <<a href="mailto:huazhong@nmsu.edu" class="">huazhong@nmsu.edu</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div id="divtagdefaultwrapper" style="font-style: normal; font-variant: 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-stroke-width: 0px; font-size: 12pt; background-color: rgb(255, 255, 255); font-family: Calibri, Arial, Helvetica, sans-serif;" class=""><div style="margin-top: 0px; margin-bottom: 0px;" class="">Hello,<br class=""></div><p style="margin: 1em 0px; padding: 0px; border: 0px; color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif; font-size: 13px;" class="">we are using maker (2.31.8) with mvapich2, but the program terminates with a segmentation fault while setting up GFF3 output and fasta chunks. We really have no idea what the problem was. </p><p style="margin: 1em 0px; padding: 0px; border: 0px; color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif; font-size: 13px;" class="">Below is the error message:<br class=""></p><div style="margin: 1em 0px; padding: 0px; border: 0px; color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif; font-size: 13px;" class=""><br class="webkit-block-placeholder"></div><div style="margin-top: 0px; margin-bottom: 0px;" class="">+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><span class="s1">setting up GFF3 output and fasta chunks</span></div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><span class="s1">setting up GFF3 output and fasta chunks</span></div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><span class="s1">setting up GFF3 output and fasta chunks</span></div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><span class="s1">setting up GFF3 output and fasta chunks</span></div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><span class="s1">setting up GFF3 output and fasta chunks</span></div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><span class="s1">setting up GFF3 output and fasta chunks</span></div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><span class="s1">[fpga04.cluster:mpi_rank_111][</span><span class="s2">error</span><span class="s1">_sighandler] Caught<span class="Apple-converted-space"> </span></span><span class="s2">error</span><span class="s1">: Segmentation fault (signal 11)</span></div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><span class="s1">[fpga04.cluster:mpi_rank_107][</span><span class="s2">error</span><span class="s1">_sighandler] Caught<span class="Apple-converted-space"> </span></span><span class="s2">error</span><span class="s1">: Segmentation fault (signal 11)</span></div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><span class="s1">Perl exited with active threads:</span></div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><span class="s1"> 1 running and unjoined</span></div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><span class="s1"> 0 finished and unjoined</span></div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><span class="s1"> 0 running and detached</span></div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><span class="s1">[fpga04.cluster:mpi_rank_113][</span><span class="s2">error</span><span class="s1">_sighandler] Caught<span class="Apple-converted-space"> </span></span><span class="s2">error</span><span class="s1">: Segmentation fault (signal 11)</span></div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><span class="s1">[fpga04.cluster:mpi_rank_115][</span><span class="s2">error</span><span class="s1">_sighandler] Caught<span class="Apple-converted-space"> </span></span><span class="s2">error</span><span class="s1">: Segmentation fault (signal 11)</span></div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><span class="s1">[fpga04.cluster:mpi_rank_114][</span><span class="s2">error</span><span class="s1">_sighandler] Caught<span class="Apple-converted-space"> </span></span><span class="s2">error</span><span class="s1">: Segmentation fault (signal 11)</span></div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><span class="s1">[fpga04.cluster:mpi_rank_105][</span><span class="s2">error</span><span class="s1">_sighandler] Caught<span class="Apple-converted-space"> </span></span><span class="s2">error</span><span class="s1">: Segmentation fault (signal 11)</span></div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><span class="s1">[fpga04.cluster:mpi_rank_108][</span><span class="s2">error</span><span class="s1">_sighandler] Caught<span class="Apple-converted-space"> </span></span><span class="s2">error</span><span class="s1">: Segmentation fault (signal 11)</span></div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><span class="s1">[fpga04.cluster:mpi_rank_110][</span><span class="s2">error</span><span class="s1">_sighandler] Caught<span class="Apple-converted-space"> </span></span><span class="s2">error</span><span class="s1">: Segmentation fault (signal 11)</span></div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><span class="s1">[fpga04.cluster:mpi_rank_104][</span><span class="s2">error</span><span class="s1">_sighandler] Caught<span class="Apple-converted-space"> </span></span><span class="s2">error</span><span class="s1">: Segmentation fault (signal 11)</span></div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><span class="s1">[fpga04.cluster:mpi_rank_106][</span><span class="s2">error</span><span class="s1">_sighandler] Caught<span class="Apple-converted-space"> </span></span><span class="s2">error</span><span class="s1">: Segmentation fault (signal 11)</span></div><span style="color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif; font-size: 13px;" class="">+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</span><br class=""><p style="margin-top: 0px; margin-bottom: 0px;" class=""></p><p style="margin: 1em 0px; padding: 0px; border: 0px; color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif; font-size: 13px;" class=""><span style="color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif; font-size: 13px;" class="">Best regards,</span></p><p style="margin: 1em 0px; padding: 0px; border: 0px; color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif; font-size: 13px;" class=""><span style="color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif; font-size: 13px;" class="">Hua</span></p><p style="margin-top: 0px; margin-bottom: 0px;" class=""></p></div><span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: 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-stroke-width: 0px; float: none; display: inline !important;" class="">_______________________________________________</span><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: 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-stroke-width: 0px;" class=""><span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: 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-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: 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-stroke-width: 0px;" class=""><a href="mailto:maker-devel@box290.bluehost.com" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: 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-stroke-width: 0px;" class="">maker-devel@box290.bluehost.com</a><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: 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-stroke-width: 0px;" class=""><a href="http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: 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-stroke-width: 0px;" class="">http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org</a></div></blockquote></div><br class=""></div></body></html>