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cluster:213 [2022/05/10 09:31]
hmeij07 		cluster:213 [2023/01/31 13:57]
hmeij07
Line 88: Line 88:
 vi /etc/selinux/config # disabled, do not mistype, kernel will not boot! vi /etc/selinux/config # disabled, do not mistype, kernel will not boot!
 mv /home /usr/local/ mv /home /usr/local/
 +cd /;ln -s /usr/local/home 
 +cd /; ln -s /home /share
 vi /etc/passwd (exx, dockeruser $HOME) vi /etc/passwd (exx, dockeruser $HOME)
  
Line 94: Line 96:
 ## cottontail2 = greentail52 sections ## cottontail2 = greentail52 sections
  
 +#exx96
 mkdir /sanscratch /home/localscratch mkdir /sanscratch /home/localscratch
 chmod ugo+rwx /sanscratch /home/localscratch chmod ugo+rwx /sanscratch /home/localscratch
 chmod o+t /sanscratch /home/localscratch  chmod o+t /sanscratch /home/localscratch 
 +# exx96
 # link localscratch in 1.4T /home to / # link localscratch in 1.4T /home to /
-mkdir /home  + 
-cd /home # local dir+cd /home 
 ln -s /zfshomes/apps ln -s /zfshomes/apps
 ln -s /zfshomes/tmp ln -s /zfshomes/tmp
 ln -s /zfshomes/csmith06 ln -s /zfshomes/csmith06
-ln -s /zfshomes /share+
  
 # fstab file mounts # fstab file mounts
 +mkdir -p /zfshomes /home66 /home33 /mindstore /opt/ohpc/pub /opt/intel
 # cottontail2 = greentail52 # cottontail2 = greentail52
 # n100-n101 = n79 # n100-n101 = n79
Line 116: Line 121:
  
 # on head node /etc/chronyc.conf # on head node /etc/chronyc.conf
-allow 192.168.0.0/6+allow 192.168.0.0/16
 # compute nodes /etc/chronyc.conf # compute nodes /etc/chronyc.conf
 #pool 2.pool.ntp.org iburst #pool 2.pool.ntp.org iburst
Line 144: Line 149:
  
 #easybuild #easybuild
-yum install libibvers libibverbs-devel+yum install libibverbs libibverbs-devel
  
 # amber20 cmake readline error fix needs # amber20 cmake readline error fix needs
Line 185: Line 190:
 # openjdk version "1.8.0_322" # openjdk version "1.8.0_322"
 rpm -qa | grep ^java  # check rpm -qa | grep ^java  # check
 +yum install java-1.8.0-openjdk java-1.8.0-openjdk-devel \
 +java-1.8.0-openjdk-headless javapackages-filesystem
 # python v 3.9 # python v 3.9
 yum install python39 python39-devel yum install python39 python39-devel
Line 198: Line 205:
 # dmtcp # dmtcp
 yum install dmtcp dmtcp-devel yum install dmtcp dmtcp-devel
 +
 +# check status of service munge
  
 yum clean all yum clean all
Line 222: Line 231:
   scp cottontail2:/etc/slurm/slurm.conf /etc/slurm/slurm.conf   scp cottontail2:/etc/slurm/slurm.conf /etc/slurm/slurm.conf
   scp cottontail2:/etc/slurm/gres.conf /etc/slurm/gres.conf   scp cottontail2:/etc/slurm/gres.conf /etc/slurm/gres.conf
 +  scp cottontail2:/etc/profile.d/lmod.sh /etc/profile.d/
 +  
 +# /var/[log|spool|run] need to be removed from
 +/usr/libexec/warewulf/wwmkchroot/gold-template
 +
 #test #test
   /usr/sbin/slurmd -D    /usr/sbin/slurmd -D 
Line 257: Line 271:
  
 <code> <code>
 +
 +# First **all the necessary packages ** (yum install...)
  
  988  tar xvfj ../AmberTools21.tar.bz2   988  tar xvfj ../AmberTools21.tar.bz2 
Line 266: Line 282:
 #  Assume this is Linux: #  Assume this is Linux:
  
-# serial, do on heasd node, pull down miniconda, compile, install+# serial, do on head node, with miniconda true, compile, install
   cmake $AMBER_PREFIX/amber20_src \   cmake $AMBER_PREFIX/amber20_src \
     -DCMAKE_INSTALL_PREFIX=/share/apps/CENTOS8/ohpc/software/amber/20 \     -DCMAKE_INSTALL_PREFIX=/share/apps/CENTOS8/ohpc/software/amber/20 \
Line 324: Line 340:
  
 </code> </code>
 +
 +==== Amber22 ====
 +
 +OpenHPC
 +
 +<code>
 +
 +# First **all the necessary packages ** (yum install...)
 +
 + 988  tar xvfj ../AmberTools22.tar.bz2 
 +  989  tar xvfj ../Amber22.tar.bz2 
 +  993  cd amber20_src/
 +  994  cd build/
 +  996  vi run_cmake
 +
 +#  Assume this is Linux:
 +
 +# serial, do on head node, with miniconda true, compile, install
 +  cmake $AMBER_PREFIX/amber22_src \
 +    -DCMAKE_INSTALL_PREFIX=/share/apps/CENTOS8/ohpc/software/amber/22 \
 +    -DCOMPILER=GNU  \
 +    -DMPI=FALSE -DCUDA=FALSE -DINSTALL_TESTS=TRUE \
 +    -DDOWNLOAD_MINICONDA=TRUE \
 +    2>&1 | tee  cmake.log
 +./run_cmake
 +make install
 +
 +
 +# Note !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
 +The OpenMPI and MPICH system installations provided by CentOS 
 +(i.e., through yum install) 
 +are known to be somehow incompatible with Amber22.
 +# OUCH !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
 +
 +
 +# GO TO node n100
 +
 +# copy head node's amber22_src/ to n100:/usr/local/src/tmp/
 +
 +
 +source /share/apps/CENTOS8/ohpc/software/amber/22/amber.sh
 +echo $AMBERHOME
 +
 +# install latest openmpi version
 +cd amber_src/Ambertools/src
 +tar xvfj ../../../../openmpi-4.1.4.tar.bz2 
 +
 +./configure_openmpi gnu # openhpc gcc/gfortran 
 +
 +
 +# on n100 now, parallel, set 
 +-MPI=TRUE
 +-DDOWNLOAD_MINICONDA=FALSE
 +./run_cmake
 +make install
 +
 +# on n100 just change cuda flag
 +
 +[hmeij@n100 build]$ module load cuda/11.6
 +[hmeij@n100 build]$ which gcc mpicc nvcc
 +/opt/ohpc/pub/compiler/gcc/9.4.0/bin/gcc
 +/share/apps/CENTOS8/ohpc/software/amber/22/bin/mpicc
 +/usr/local/cuda/bin/nvcc
 +[hmeij@n100 ~]$ echo $CUDA_HOME
 +/usr/local/cuda
 +
 +-MPI=TRUE
 +-CUDA=TRUE
 +-DDOWNLOAD_MINICONDA=FALSE
 +./run_cmake
 +make install
 +
 +
 +[hmeij@n100 ~]$ which nvcc mpicc gcc
 +/usr/local/cuda/bin/nvcc
 +/opt/ohpc/pub/mpi/openmpi4-gnu9/4.1.1/bin/mpicc
 +/opt/ohpc/pub/compiler/gcc/9.4.0/bin/gcc
 +
 +#tests
 +cd $AMBERHOME
 +make test.serial
 +export DO_PARALLEL="mpirun -np 6"
 +make test.parallel
 +export CUDA_VISIBLE_DEVICES=0
 +make test.cuda.serial
 +make test.cuda.parallel
 +
 +</code>
 +
  
 **[[cluster:0|Back]]** **[[cluster:0|Back]]**
  
cluster/213.txt · Last modified: 2024/01/12 10:09 by hmeij07

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