• relion-3.1
    #%Module1.0
    conflict eman2
    module load mpi
     
    set RELION /apps/relion-3.1
    prepend-path PATH            $RELION/bin
     
    setenv RELION_QSUB_COMMAND   qsub
    setenv RELION_MPIRUN         mpirun
    setenv RELION_QSUB_TEMPLATE  $RELION/bin/qsub.sh
    setenv RELION_QUEUE_NAME     s3
    setenv RELION_QUEUE_USE      false
     
    setenv RELION_QSUB_NRTHREADS         4
    setenv RELION_THREAD_MAX             16
    setenv RELION_QSUB_NRMPI             4
    setenv RELION_MPI_MAX                32
    setenv RELION_ERROR_LOCAL_MPI        32    #ローカルで32mpiより多く指定して計算するとエラー掲示
    setenv RELION_SHELL                  csh   # ctffindを外部コールに使用するSHELL
    setenv RELION_EXTERNAL_RECONSTRUCT_EXECUTABLE relion_external_reconstruct
     
    setenv RELION_CTFFIND_EXECUTABLE     /apps/ctffind-4.1.13/bin/ctffind
    setenv RELION_MOTIONCOR2_EXECUTABLE  /apps/MotionCor2/MotionCor2_1.3.0-Cuda101
    setenv RELION_GCTF_EXECUTABLE        /apps/Gctf/Gctf-v1.06_sm_30_cu8.0_x86_64
    setenv RELION_RESMAP_EXECUTABLE      /apps/ResMap/ResMap-1.1.4-linux64
    setenv RELION_PDFVIEWER_EXECUTABLE   evince
    setenv RELION_SCRATCH_DIR            \$TMPDIR    # scratchの場所. pbsproのTMPDIRを使うなら
     
    setenv RELION_EXTERNAL_RECONSTRUCT_EXECUTABLE /apps/SIDESPLITTER/sidesplitter_wrapper.sh
    setenv SIDESPLITTER                           /apps/SIDESPLITTER/sidesplitter
  • relion-3.0.8
    #%Module1.0
    conflict eman2
    module load mpi
     
    set RELION /apps/relion-3.0.8
    prepend-path PATH            $RELION/bin
     
    setenv RELION_QSUB_COMMAND   qsub
    setenv RELION_MPIRUN         mpirun
    setenv RELION_QSUB_TEMPLATE  $RELION/bin/qsub.sh
    setenv RELION_QUEUE_NAME     s3
    setenv RELION_QUEUE_USE      false
     
    setenv RELION_CTFFIND_EXECUTABLE     /apps/ctffind-4.1.13/bin/ctffind
    setenv RELION_MOTIONCOR2_EXECUTABLE  /apps/MotionCor2/MotionCor2_1.3.0-Cuda101
    setenv RELION_GCTF_EXECUTABLE        /apps/Gctf/Gctf-v1.06_sm_30_cu8.0_x86_64
    setenv RELION_RESMAP_EXECUTABLE      /apps/ResMap/ResMap-1.1.4-linux64
    setenv RELION_PDFVIEWER_EXECUTABLE   evince
    setenv RELION_UNBLUR_EXECUTABLE      /apps/unblur_1.0.2/bin/unblur_openmp_7_17_15.exe
    setenv RELION_SUMMOVIE_EXECUTABLE    /apps/summovie_1.0.2/bin/sum_movie_openmp_7_17_15.exe
  • relion-2.1
    #%Module1.0
    conflict eman2
    module load mpi
     
    set RELION /apps/relion-2.1
    prepend-path PATH            $RELION/bin
     
    setenv RELION_QSUB_TEMPLATE  $RELION/bin/qsub.sh
    setenv RELION_QUEUE_NAME     s3
    setenv RELION_QUEUE_USE      false
     
    setenv RELION_CTFFIND_EXECUTABLE     /apps/ctffind-4.1.13/bin/ctffind
    setenv RELION_MOTIONCOR2_EXECUTABLE  /apps/MotionCor2/MotionCor2_1.3.0-Cuda101
    setenv RELION_GCTF_EXECUTABLE        /apps/Gctf/Gctf-v1.06_sm_30_cu8.0_x86_64
    setenv RELION_RESMAP_EXECUTABLE      /apps/ResMap/ResMap-1.1.4-linux64
    setenv RELION_PDFVIEWER_EXECUTABLE   evince
    setenv RELION_UNBLUR_EXECUTABLE      /apps/unblur_1.0.2/bin/unblur_openmp_7_17_15.exe
    setenv RELION_SUMMOVIE_EXECUTABLE    /apps/summovie_1.0.2/bin/sum_movie_openmp_7_17_15.exe
  • eman2.31
    #%Module1.0
    conflict mpi
    conflict eman2
     
    set EMAN2DIR /apps/eman2.31
     
    setenv EMAN2DIR $EMAN2DIR
    prepend-path PATH $EMAN2DIR/bin
    *eman2.31自身が提供するpython[$EMAN2DIR/bin/python](2.7.15)があるので要注意
    *eman2.31自身が提供するmpirun[$EMAN2DIR/bin/mpirun](3.1.3)があるので要注意
  • eman2.12
    #%Module1.0
    conflict eman2
     
    set EMAN2DIR /apps/eman2.12
     
    setenv EMAN2DIR $EMAN2DIR
    prepend-path PATH       $EMAN2DIR/bin:$EMAN2DIR/extlib/bin
    prepend-path PYTHONPATH $EMAN2DIR/lib:$EMAN2DIR/bin
    *eman2.12自身が提供するpython[$EMAN2DIR/extlib/bin/python](2.7.3)があるので要注意
  • phenix
    #%Module1.0
    #
    set phenix /apps/phenix-1.17.1-3660
    #
    setenv PHENIX $phenix
    setenv PHENIX_VERSION  1.17.1-3660
    prepend-path PATH $phenix/build/bin
    *phenix自身が提供するpython(2.7.15)があるので要注意
  • coot
    *PATH環境変数で定義するとcootのpythonが優勢になるので、エイリアスで対応
    #%Module1.0
    #
    set-alias coot /apps/coot-Linux-x86_64-rhel-6-pre-release-gtk2-python/bin/coot
    # ccpemのcoot 0.9-preなら
    # set-alias coot /apps/ccpem-1.4.1/bin/coot
  • pymol
    #%Module1.0
    set pymol /apps/pymol
    set-alias pymol $pymol/bin/pymol
    #
    #「freeglut  ERROR:  Internal error <FBConfig with necessary capabilities not found> in function fgOpenWindow」が表示されるなら
    setenv LIBGL_ALWAYS_INDIRECT 1
  • Fiji
    #%Module1.0
    set-alias Fiji /apps/Fiji.app/ImageJ-linux64
    set-alias fiji /apps/Fiji.app/ImageJ-linux64
  • Gautomatch
    #%Module1.0
    set-alias Gautomatch /apps/Gautomatch/v0.56/Gautomatch
    set-alias gautomatch /apps/Gautomatch/v0.56/Gautomatch
  • chimera
    #%Module1.0
    set-alias chimera /apps/chimera-1.14/bin/chimera
  • bsoft
    #%Module1.0
    set bsoft /apps/bsoft
    setenv BSOFT $bsoft
    setenv BPARAM $bsoft/parameters/
     
    prepend-path PATH $bsoft/bin
    prepend-path LD_LIBRARY_PATH $bsoft/lib
  • SPRING
    #%Module1.0
    #
    prepend-path PATH /apps/spring_v0-86-1661/bin
  • cisTEM
    #%Module1.0
    #
    prepend-path PATH /apps/cistem-1.0.0-beta
  • crYOLO
    #%Module -*- tcl -*-
    ##
    ## dot modulefile
    ##
    proc ModulesHelp { } {
     
      puts stderr "\tAdds anaconda to your environment variables,"
    }
    module-whatis "Adds anaconda to your environment variables"
    set               root              /apps/pyenv/versions/anaconda3-5.3.1/envs/cryolo
    setenv CRYOLOPATH $root
    prepend-path      PATH              $root/bin
  • scipion
    #%Module1.0
     
    setenv CONDA_ACTIVATION_CMD "source /apps/pyenv/versions/anaconda3-5.3.1/etc/profile.d/conda.sh"
    set-alias scipion /apps/scipion/scipion
  • IMOD
    #%Module1.0
    #
    set imod     /apps/IMOD
    #
    prepend-path PATH            $imod/bin
    prepend-path LD_LIBRARY_PATH $imod/lib
    prepend-path MANPATH         $imod/man
     
     
    setenv IMOD_DIR        $imod
    setenv IMOD_QTLIBDIR   $imod/qtlib
    setenv IMOD_PLUGIN_DIR $imod/lib/imodplug
    #setenv IMOD_JAVADIR    /usr/lib/jvm/java-1.8.0-openjdk-1.8.0.191.b12-1.el7_6.x86_64/jre/bin/
    setenv IMOD_JAVADIR    /usr
    setenv FOR_DISABLE_STACK_TRACE 1
    setenv IMOD_CALIB_DIR  $imod/autodoc
  • ccp4-7
    #%Module1.0
    #
    puts stdout "source /apps/local/bin/ccp4-mkdir;"
    #
    set ccp4_master /apps
    set ccp4        $ccp4_master/ccp4-7.0
    set warp        $ccp4_master/arp_warp_8.0
    #
    setenv CCP4_MASTER $ccp4_master
    setenv CCP4        $ccp4
    setenv CBIN        $ccp4/bin
    setenv CLIB        $ccp4/lib
    setenv CLIBD       $ccp4/lib/data
    setenv CINCL       $ccp4/include
    setenv CETC        $ccp4/etc
    setenv CHTML       $ccp4/html
    setenv CEXAM       $ccp4/examples
    setenv CCP4I_TCLTK $ccp4/bin
    setenv CCP4_HELPDIR $ccp4/help/
    setenv CLIBD_MON   $ccp4/lib/data/monomers/
    setenv CCP4_OPEN   UNKNOWN
    setenv CCP4_SCR    /tmp/$env(USER)
     
    setenv CRANK       $ccp4/share/ccp4i/crank
    setenv CCP4I_TOP   $ccp4/share/ccp4i
     
    setenv warpbin     $warp/bin/bin-x86_64-Linux
    setenv warpdoc     $warp/manual
     
    setenv MMCIFDIC    $ccp4/lib/ccp4/cif_mmdic.lib
    setenv SSL_CERT_FILE $ccp4/etc/ssl/cacert.pem
     
    prepend-path PATH  $warp/bin/bin-x86_64-Linux:$ccp4/etc:$ccp4/bin
    prepend-path MANPATH $ccp4/share/man
     
    setenv GFORTRAN_UNBUFFERED_PRECONNECTED Y
    /apps/local/bin/ccp4-mkdir
    #!/bin/bash
    if [ ! -d /tmp/$USER ]; then
       /bin/mkdir /tmp/$USER
    fi
  • ccpem
    #%Module1.0
     
    module load ccp4/7.0
     
    set ccpem /Appl/ccpem-1.4.1
    setenv CCPEM $ccpem
     
    prepend-path PATH $ccpem/bin
    prepend-path LD_LIBRARY_PATH $ccpem/lib/modeller/install/lib/x86_64-intel8
  • icc
    #%Module1.0
    #
    set icc /opt/intel/compilers_and_libraries/linux
    set tbb $icc/tbb/lib/intel64/gcc4.7
    set mpi $icc/mpi/intel64/libfabric/lib:$icc/mpi/intel64/lib/releas:$icc/mpi/intel64/lib
    set mkl $icc/mkl/lib/intel64
    #
    setenv INTEL_LICENSE_FILE /opt/intel/licenses
    #
    setenv MKLROOT            $icc/mkl
    setenv TBBROOT            $icc/tbb
    setenv PSTLROOT           $icc/pstl
    setenv I_MPI_ROOT         $icc/mpi
    #
    setenv FI_PROVIDER_PATH   $icc/mpi/intel64/libfabric/lib/prov
    setenv CPATH              $icc/mkl/include:$icc/pstl/include:$icc/tbb/include
    setenv NLSPATH            $icc/lib/intel64/locale/%l_%t/%N:$icc/mkl/lib/intel64/locale/%l_%t/%N
     
    prepend-path PATH            $icc/bin/intel64:$icc/mpi/intel64/libfabric/bin:$icc/mpi/intel64/bin
    prepend-path LIBRARY_PATH    $icc/lib/intel64:$mpi:$mkl:$tbb  
    prepend-path LD_LIBRARY_PATH $icc/lib/intel64:$mpi:$mkl:$tbb  
    prepend-path MANPATH         /opt/intel/man/common:$icc/mpi/man
    prepend-path CLASSPATH       $icc/mpi/intel64/lib/mpi.jar
    prepend-path PKG_CONFIG_PATH $icc/mkl/bin/pkgconfig
  • iccRuntime
    #%Module1.0
    #
    set icc /opt/intel/psxe_runtime_2019.4.243/linux
    set tbb $icc/tbb/lib/intel64/gcc4.7
    set mpi $icc/mpi/intel64/libfabric/lib:$icc/mpi/intel64/lib/release:$icc/mpi/intel64/lib
    set mkl $icc/mkl/lib/intel64
    set cmp $icc/compiler/lib/intel64_lin
    #
    setenv I_MPI_ROOT             $icc/mpi
    setenv FI_PROVIDER_PATH       $icc/mpi/intel64/libfabric/lib/prov
    #
    prepend-path PATH             $icc/mpi/intel64/libfabric/bin:$icc/mpi/intel64/bin
    prepend-path LIBRARY_PATH     $icc/mpi/intel64/libfabric/lib
    prepend-path LD_LIBRARY_PATH  $mpi:$mkl:$cmp:$tbb
    prepend-path MANPATH          $icc/mpi/man
    prepend-path CLASSPATH        $icc/mpi/intel64/lib/mpi.jar

使っているshellで分ける

bashとcshで「RELION_QSUB_TEMPLATE」を分けるとかできそう

#%Module1.0
 
 
if { $env(SHELL) == "/bin/bash" } {
  setenv RELION_QSUB_TEMPLATE $RELION/bin/qsub.sh
} elseif { $env(SHELL) == "/bin/csh" } {
  setenv RELION_QSUB_TEMPLATE $RELION/bin/qsub.csh
} elseif { $env(SHELL) == "/bin/tcsh" } {
  setenv RELION_QSUB_TEMPLATE $RELION/bin/qsub.csh
}

そうすると、qsub.sh/qsub.cshを用意する必要があるけど、特にqsub.csh内でmodule loadが使えるようになる


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Last-modified: 2020-04-08 (水) 21:36:37 (2d)