<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="">The problem is the actual MPICH2 installation. You may be missing prerequisites or you may not have compiled with the necessary shared library flags (-enable-shared). You may also be compiling on one machine that has certain libraries installed then running on another that doesn’t have access to those libraries (this can happen if running on a cluster). Try reinstalling MPICH2 or switching to OpenMPI.<div class=""><br class=""></div><div class="">If you decide to use OpenMPI, <span style="color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif; font-size: 13px;" class="">he following is from the INSTALL file that should be included with MAKER —></span></div><div style="margin: 0px; padding: 0px; border: 0px; color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif; font-size: 13px;" class=""><br class=""></div><span style="color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif; font-size: 13px; background-color: rgb(255, 255, 255);" class="">If using OpenMPI, make sure to set LD_PRELOAD to the location of libmpi.so before even trying to install MAKER. </span><b style="color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif; font-size: 13px;" class="">It must also be set before running MAKER</b><span style="color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif; font-size: 13px; background-color: rgb(255, 255, 255);" class=""> (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 style="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; background-color: rgb(255, 255, 255);" class="">location/of/openmpi/lib/</span><wbr style="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; background-color: rgb(255, 255, 255);" class="">libmpi.so).</span><br style="color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif; font-size: 13px;" class=""><br style="color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif; font-size: 13px;" class=""><br style="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; background-color: rgb(255, 255, 255);" class="">1. Say yes to the 'configure for MPI' question when running 'perl Build.PL’ in step 1 of the EASY INSTALL.</span><br style="color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif; font-size: 13px;" class=""><br style="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; background-color: rgb(255, 255, 255);" class="">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 style="color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif; font-size: 13px;" class=""><br style="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; background-color: rgb(255, 255, 255);" class="">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 style="color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif; font-size: 13px;" class=""><br style="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; background-color: rgb(255, 255, 255);" class="">4. Finish installation according to steps 2-4 of the EASY INSTALL</span><br style="color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif; font-size: 13px;" class=""><br style="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; background-color: rgb(255, 255, 255);" class="">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 style="color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif; font-size: 13px;" class=""><br style="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; background-color: rgb(255, 255, 255);" class="">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 style="color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif; font-size: 13px;" class=""><br style="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; background-color: rgb(255, 255, 255);" class=""> Example: mpiexec -mca btl ^openib -n 20 maker</span><div class=""><br class=""></div><div class="">Thanks,</div><div class="">Carson</div><div class=""><br class=""></div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On Nov 5, 2015, at 12:16 AM, Anna Nyiri <<a href="mailto:dancsi90@gmail.com" class="">dancsi90@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class=""><div class=""><div class=""><div class=""><div class=""><div class="">Hi,<br class=""><br class=""></div>I tried to use MAKER with MPICH2, but I got an error message:<br class="">"/molbio/bin/danna/mpich2-install/bin/hydra_pmi_proxy: error while loading shared libraries: libtorque.so.2: cannot open shared object file: No such file or directory"<br class=""><br class=""></div>The attached file contains the shell sctipt, which I used. Is this script correct?<br class=""><br class=""></div>The script should contain MPICH module. But I can't find it on my computer. Where can I find this module?<br class=""><br class=""></div>Thanks for your help,<br class=""></div>Anna Nyiri<br class=""></div>
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