EnvironmentModules/sample

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

EnvironmentModules/sample

使っているshellで分ける †

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