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cluster:213 [2022/05/12 09:11]
hmeij07 		cluster:213 [2023/01/31 14:37]
hmeij07
Line 73: Line 73:
 iptables -L # check! iptables -L # check!
  
-# Rocky8 +
-# https://docs.fedoraproject.org/en-US/epel/#Quickstart +
-dnf config-manager --set-enabled powertools +
-dnf install epel-release +
-dnf install netcdf netcdf-devel +
-dnf install yum-utils # yumdownloader +
-dnf install ddd  +
-dnf install grace +
-dnf install gnuplot +
-dnf install alpine # pico +
-yum groupinstall "Server" # server for compute nodes "Server with GUI"+
  
 # other configs # other configs
 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)
  
-## edit passwd, shadow, group, hosts files ## 
-## make -orig backups and stage in /home/tmp/global 
-## 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
  
-# postfix 
-dnf install postfix 
-dnf install mailx 
-systemctl enable postfix 
-echo "relayhost = 192.168.102.251" >> /etc/postfix/main.cf 
  
 # on head node /etc/chronyc.conf # on head node /etc/chronyc.conf
Line 123: Line 110:
 # check # check
 chronyc sources chronyc sources
 +
 +# Rocky8
 +# https://docs.fedoraproject.org/en-US/epel/#Quickstart
 +dnf config-manager --set-enabled powertools
 +dnf install epel-release
 +dnf install netcdf netcdf-devel
 +dnf install yum-utils # yumdownloader
 +dnf install ddd 
 +dnf install grace
 +dnf install gnuplot
 +dnf install alpine # pico
 +yum groupinstall "Server" # server for compute nodes "Server with GUI"
  
  
Line 168: Line 167:
 # compute nodes old level 3 # compute nodes old level 3
 systemctl set-default multi-user.target systemctl set-default multi-user.target
 +
 +
 +# postfix
 +dnf install postfix
 +dnf install mailx
 +systemctl enable postfix
 +echo "relayhost = 192.168.102.251" >> /etc/postfix/main.cf
 +
 +yum install net-snmp-utils net-snmp-libs net-snmp net-snmp-agent-libs
 +
 +# edit /etc/snmp/snmpd.conf, enable and start
 +rocommunity public
 +dontLogTCPWrappersConnects yes
 +# enable, start, add to zenoss 
 +
  
 # compute nodes only # compute nodes only
Line 201: Line 215:
 yum install dmtcp dmtcp-devel yum install dmtcp dmtcp-devel
  
-# check status of service munge+
  
 yum clean all yum clean all
Line 214: Line 228:
   scp cottontail2:/etc/resolv.conf /etc/resolv.conf   scp cottontail2:/etc/resolv.conf /etc/resolv.conf
   yum  install ohpc-slurm-client   yum  install ohpc-slurm-client
 +  # check status of service munge
   systemctl enable munge   systemctl enable munge
   systemctl start munge   systemctl start munge
Line 239: Line 254:
 sleep 15 sleep 15
 /usr/sbin/slurmd /usr/sbin/slurmd
 +
 +
 +## edit passwd, shadow, group, hosts files ##
 +## make -orig backups and stage in /home/tmp/global
 +## cottontail2 = greentail52 sections
 +
      
 # slurmd ??? # slurmd ???
  libhwloc.so.15 => /opt/ohpc/pub/libs/hwloc/lib/libhwloc.so.15 (0x00007fd6e5684000)  libhwloc.so.15 => /opt/ohpc/pub/libs/hwloc/lib/libhwloc.so.15 (0x00007fd6e5684000)
  
-# add to zenoss edit /etc/snmp/snmpd.conf, enable and start +
-rocommunity public +
-dontLogTCPWrappersConnects yes+
  
 </code> </code>
Line 266: Line 285:
  
 <code> <code>
 +
 +# First **all the necessary packages ** (yum install...)
  
  988  tar xvfj ../AmberTools21.tar.bz2   988  tar xvfj ../AmberTools21.tar.bz2 
Line 275: Line 296:
 #  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 333: Line 354:
  
 </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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