• 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
  • 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
#あるいは
/bin/rm -rf /tmp/$USER
/bin/mkdir  /tmp/$USER
  • ccpem 
    #%Module1.0
 
module load ccp4/7.1
 
set ccpem /apps/ccpem-1.5.0
setenv CCPEM $ccpem
 
prepend-path PATH $ccpem/bin
prepend-path LD_LIBRARY_PATH $ccpem/lib/modeller/install/lib/x86_64-intel8
  • chimera 
    #%Module1.0
set-alias chimera /apps/chimera-1.15/bin/chimera
  • cinderella 
    #%Module
set          root /apps/pyenv/versions/anaconda3-5.3.1/envs/cinderella
prepend-path PATH $root/bin
  • cisTEM 
    #%Module1.0
prepend-path PATH /apps/cistem-1.0.0-beta
  • 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-scientific-linux-7.6-gtk2-python/bin/coot
# ccpemのcoot 0.9-preなら
# set-alias coot /apps/ccpem-1.5.0/bin/coot
  • cryoDRGN 
    #%Module -*- tcl -*-
set          root /apps/pyenv/versions/anaconda3-5.3.1/envs/cryodrgn
prepend-path PATH $root/bin
  • crYOLO 
    #%Module
set          root       /apps/pyenv/versions/anaconda3-5.3.1/envs/cryolo
setenv       CRYOLOPATH $root
prepend-path PATH       $root/bin
  • deepEMhancer 
    #%Module1.0
set          root /apps/pyenv/versions/anaconda3-5.3.1/envs/deepEMhancer_env/
prepend-path PATH $root/bin
  • EM2EM 
    #%Module1.0
set-alias em2em /apps/EM2EM/guiEM2EM.AppImage
  • eman2.91
    「/etc/modulefiles/eman2/2.91」 
    #%Module1.0
set          EMAN2DIR        /apps/eman2.91
setenv       EMAN2DIR        $EMAN2DIR
prepend-path PATH            $EMAN2DIR/bin
prepend-path LD_LIBRARY_PATH $EMAN2DIR/lib
  • eman2.31 
    #%Module1.0
set          EMAN2DIR /apps/eman2.31
setenv       EMAN2DIR $EMAN2DIR
prepend-path PATH     $EMAN2DIR/bin
  • eman2.12 
    #%Module1.0
set          EMAN2DIR   /apps/eman2.12
setenv       EMAN2DIR   $EMAN2DIR
prepend-path PATH       $EMAN2DIR/bin:$EMAN2DIR/extlib/bin
prepend-path PYTHONPATH $EMAN2DIR/lib:$EMAN2DIR/bin
  • EPU_group_AFIS 
    #%Module1.0
set          EPU_group_AFIS /apps/EPU_group_AFIS
set          root           /apps/pyenv/versions/anaconda3-5.3.1/envs/EPU_group_AFIS
prepend-path PATH           $EPU_group_AFIS:$root/bin
  • 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/GCTF_Gautomatch_Cu10.1/Gautomatch_v0.56_sm30-75_cu10.1
set-alias gautomatch /apps/GCTF_Gautomatch_Cu10.1/Gautomatch_v0.56_sm30-75_cu10.1
  • Gctf 
    #%Module1.0
set-alias Gctf /apps/GCTF_Gautomatch_Cu10.1/GCTF_v1.18_sm30-75_cu10.1
set-alias gctf /apps/GCTF_Gautomatch_Cu10.1/GCTF_v1.18_sm30-75_cu10.1
  • 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
 
set-alias subm "submfg \!* &"
    *「set-alias subm 'submfg \!* &'」でエラーになる場合があるので、素直に「source /apps/IMOD/IMOD-linux.sh」がいいかもしれない
  • janni 
    #%Module
set          root /apps/pyenv/versions/anaconda3-5.3.1/envs/janni
prepend-path PATH $root/bin
  • MotionCor2 
    #%Module
set-alias MotionCor2 /apps/MotionCor2/MotionCor2_1.4.2_Cuda111-02-15-2020
set-alias motioncor2 /apps/MotionCor2/MotionCor2_1.4.2_Cuda111-02-15-2020
  • phenix 
    #%Module1.0
set phenix /apps/phenix-1.19.2-4158
setenv PHENIX $phenix
setenv PHENIX_VERSION 1.19.2-4158
prepend-path PATH $phenix/build/bin
  • PyEM 
    #%Module1.0
set PyEM /apps/PyEM/
set root /apps/pyenv/versions/anaconda3-5.3.1/envs/PyEM
prepend-path PATH $PyEM:$root/bin
  • 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
  • PyTom 
    #%Module -*- tcl -*-
set    root  /apps/pyenv/versions/anaconda3-5.3.1/envs/PyTom
set    PYTOM /apps/pytom
prepend-path PATH            $PYTOM/bin:$root/bin
prepend-path LD_LIBRARY_PATH $PYTOM/external/lib
prepend-path PYTHONPATH      $PYTOM
  • relion-3.1.2 
    #%Module1.0
module load mpi
 
set RELION /apps/relion-3.1.2
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-4.1.14/bin/ctffind
setenv RELION_MOTIONCOR2_EXECUTABLE  /apps/MotionCor2/MotionCor2_1.4.2_Cuda111-02-15-2020
setenv RELION_GCTF_EXECUTABLE        /apps/GCTF_Gautomatch_Cu10.1/GCTF_v1.18_sm30-75_cu10.1
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
  • ResMap 
    #%Module1.0
set-alias ResMap /apps/ResMap/ResMap-1.1.4-linux64
set-alias resmap /apps/ResMap/ResMap-1.1.4-linux64
  • Scipion3 
    #%Module1.0
set-alias scipion3 /apps/scipion/scipion3
  • SPRING 
    #%Module1.0
#
prepend-path PATH /apps/spring_v0-86-1661/bin
  • topaz 
    #%Module1.0
set          root /apps/pyenv/versions/anaconda3-5.3.1/envs/topaz
prepend-path PATH $root/bin
  • xds 
    #%Module1.0
prepend-path PATH /apps/xds
  • xtal 
    #%Module1.0
 
prepend-path PATH /apps/xds:/apps/xds/xdsme/bin/noarch:/apps/xtal

icc †

  • 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        tcp
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            tcp
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
  • mklRuntime 
    #%Module1.0
#
set icc /opt/intel/compilers_and_libraries_2020.2.254/linux
#
setenv INTEL_LICENSE_FILE $icc/licenses:/opt/intel/licenses
#
setenv MKLROOT            $icc/mkl
setenv TBBROOT            $icc/tbb
#
setenv CPATH              $icc/mkl/include:$icc/tbb/include
setenv NLSPATH            $icc/compiler/lib/intel64/locale/%l_%t/%N:$icc/mkl/lib/intel64_lin/locale/%l_%t/%N
setenv LIBRARY_PATH       $icc/compiler/lib/intel64_lin:$icc/mkl/lib/intel64_lin:$icc/tbb/lib/intel64/gcc4.8
#
prepend-path PATH            $icc/bin/intel64:$icc/bin
prepend-path LD_LIBRARY_PATH $icc/compiler/lib/intel64_lin:$icc/mkl/lib/intel64_lin:$icc/tbb/lib/intel64/gcc4.8
prepend-path PKG_CONFIG_PATH $icc/mkl/bin/pkgconfig
  • oneAPI 
    #%Module1.0
#
set oneapi /opt/intel/oneapi
#
set icc           $oneapi/compiler/2021.4.0
set icc-lib       $icc/linux/lib
set icc-lib-ld    $icc-lib:$icc-lib/x64:$icc-lib/emu:$icc-lib/oclfpga/host/linux64/lib:$icc-lib/oclfpga/linux64/lib:$icc/linux/compiler/lib/intel64_lin
set icc-bin       $icc/linux/lib/oclfpga/llvm/aocl-bin:$icc/linux/lib/oclfpga/bin:$icc/linux/bin/intel64:$icc/linux/bin
set tbb           $oneapi/tbb/2021.4.0
set mkl           $oneapi/mkl/2021.4.0
set debugger      $oneapi/debugger/10.2.4
set debugger-lib  $debugger/gdb/intel64/lib:$debugger/libipt/intel64/lib:$debugger/dep/lib
set dev-utilities $oneapi/dev-utilities/2021.4.0
#####################################################
setenv ONEAPI_ROOT $oneapi
setenv TBBROOT     $tbb
setenv CMPLR_ROOT  $icc
setenv MKLROOT     $mkl
setenv INTELFPGAOCLSDKROOT $icc-lib/oclfpga
setenv INTEL_PYTHONHOME $debugger/10.2.4/dep
setenv GDB_INFO     $debugger/documentation/info/
setenv INFOPATH    $debugger/gdb/intel64/lib
setenv CMAKE_PREFIX_PATH $tbb
setenv SETVARS_VARS_PATH $tbb/env/vars.sh
setenv OCL_ICD_FILENAMES libintelocl_emu.so:libalteracl.so:$icc-lib/x64/libintelocl.so
setenv FPGA_VARS_DIR  $icc-lib/oclfpga
#####################################################
prepend-path MANPATH         $debugger/documentation/en/man/common:$debugger
prepend-path LIBRARY_PATH    $tbb/lib/intel64/gcc4.8:$mkl/lib/intel64:$icc/linux/compiler/lib/intel64_lin:$icc-lib
prepend-path LD_LIBRARY_PATH $tbb/lib/intel64/gcc4.8:$mkl/lib/intel64:$debugger-lib:$icc-lib-ld
prepend-path CPATH           $tbb/include:$mkl/include:$dev-utilities/include:$icc/linux/include
prepend-path NLSPATH         $mkl/lib/intel64/locale/%l_%t/%N
prepend-path PATH            $mkl/bin/intel64:$dev-utilities/bin:$debugger/gdb/intel64/bin:$icc-bin
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Last-modified: 2021-10-09 (土) 02:58:49 (105d)