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--- cluster:213 [2022/03/21 20:11]
hmeij07 [Pics]
+++ cluster:213 [2023/02/09 14:55]
hmeij07
@@ Line 44: / Line 44: @@
 # Put the warewulf cluster key in authorized_keys
+# Put eth0 fingerprints in cottontail/greentail52 known hosts
+# add to relevant known_hosts_servername file
 # configure private subnets and ping file server
@@ Line 71: / Line 73: @@
 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
 # other configs
 vi /etc/selinux/config # disabled, do not mistype, kernel will not boot!
 mv /home /usr/local/
+cd /;ln -s /usr/local/home
+cd /; ln -s /home /share
 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
 chmod ugo+rwx /sanscratch /home/localscratch
 chmod o+t /sanscratch /home/localscratch
+# exx96
 # link localscratch in 1.4T /home to /
-mkdir /home
-cd /home # local dir
+cd /home
 ln -s /zfshomes/apps
 ln -s /zfshomes/tmp
 ln -s /zfshomes/csmith06
-ln -s /zfshomes /share
+cat /sanscratch/tmp/fstab.tmp >> /etc/fstab; mkdir /astrostore; mount -a; df -h; cd /smithlab/;  ln -s /smithlab/home/opt/rhel08 opt; ls -l
 # fstab file mounts
+mkdir -p /zfshomes /home66 /home33 /mindstore /opt/ohpc/pub /opt/intel
 # cottontail2 = greentail52
 # 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
-allow 192.1668.0.0/6
+allow 192.168.0.0/16
 # compute nodes /etc/chronyc.conf
 #pool 2.pool.ntp.org iburst
@@ Line 120: / Line 111: @@
 # check
 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"
+# on head node install from epel repo
+### yum install slurm-openlava
+# error on conflicting libs, too bad!
@@ Line 134: / Line 142: @@
 yum install cmake -y
 yum install libjpeg libjpeg-devel libjpeg-turbo-devel -y
-# amber
+#easybuild
+yum install libibverbs libibverbs-devel
+# amber20 cmake readline error fix needs
+yum install ncurses-c++-libs-6.1-9.20180224.el8.x86_64.rpm \
+            ncurses-devel-6.1-9.20180224.el8.x86_64.rpm \
+            readline-devel-7.0-10.el8.x86_64.rpm
+# amber20
 yum -y install tcsh make \
                gcc gcc-gfortran gcc-c++ \
@@ Line 151: / Line 168: @@
 # compute nodes old level 3
 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
@@ Line 168: / Line 200: @@
 # openjdk version "1.8.0_322"
 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
 yum install python39 python39-devel
+ln -s /usr/bin/python3.9 /usr/bin/python
 # fftw 3.3.5-11.el8
 yum install fftw fftw-devel
@@ Line 180: / Line 215: @@
 # dmtcp
 yum install dmtcp dmtcp-devel
 yum clean all
@@ Line 188: / Line 225: @@
 # now make it an ohpc compute node
   yum repolist
-  yum  install ohpc-base-compute
+  yum install singularity-ohpc
+  yum  install ohpc-base-compute --nobest
   scp cottontail2:/etc/resolv.conf /etc/resolv.conf
   yum  install ohpc-slurm-client
+  # check status of service munge
   systemctl enable munge
-  scp cottontail2:/etc/munge/munge.keys /etc/munge.keys
+  systemctl start munge
+  scp cottontail2:/etc/munge/munge.key /etc/munge/munge.key
   echo SLURMD_OPTIONS="--conf-server 192.168.102.250" > /etc/sysconfig/slurmd
   yum  install --allowerasing lmod-ohpc
@@ Line 201: / Line 241: @@
   mkdir /var/spool/slurm
   chown slurm:munge /var/spool/slurm
+  scp cottontail2:/etc/slurm/slurm.conf /etc/slurm/slurm.conf
+  scp cottontail2:/etc/slurm/gres.conf /etc/slurm/gres.conf
+  scp cottontail2:/etc/profile.d/lmod.sh /etc/profile.d/
+# /etc/bashrc add
+# ohpc lmod gcc mpicc
+export PATH=/usr/local/slurm/bin:$PATH
+export LD_LIBRARY_PATH=/usr/local/slurm/lib:$LD_LIBRARY_PATH
+# /var/[log|spool|run] need to be removed from
+/usr/libexec/warewulf/wwmkchroot/gold-template
+#test
+  /usr/sbin/slurmd -D
 # start via rc.local
@@ Line 207: / Line 262: @@
 sleep 15
 /usr/sbin/slurmd
+## edit passwd, shadow, group, hosts files ##
+## make -orig backups and stage in /home/tmp/global
+## cottontail2 = greentail52 sections
 # slurmd ???
 	libhwloc.so.15 => /opt/ohpc/pub/libs/hwloc/lib/libhwloc.so.15 (0x00007fd6e5684000)
+# crontab
+# ionice gaussian
+,15,30,45 * * * * /share/apps/scripts/ionice_lexes.sh  > /dev/null 2>&1
+# cpu temps
+* * * * /share/apps/scripts/lm_sensors.sh > /dev/null 2>&1
+# file date_ctt2.sh
+# ctt /etc/pdsh
+# ctt:/root/scripts
 </code>
@@ Line 226: / Line 300: @@
 \\
+==== Amber20 ====
+OpenHPC
+<code>
+# First **all the necessary packages ** (yum install...)
+  tar xvfj ../AmberTools21.tar.bz2
+  tar xvfj ../Amber20.tar.bz2
+  cd amber20_src/
+  cd build/
+  vi run_cmake
+#  Assume this is Linux:
+# serial, do on head node, with miniconda true, compile, install
+  cmake $AMBER_PREFIX/amber20_src \
+    -DCMAKE_INSTALL_PREFIX=/share/apps/CENTOS8/ohpc/software/amber/20 \
+    -DCOMPILER=GNU  \
+    -DMPI=FALSE -DCUDA=FALSE -DINSTALL_TESTS=TRUE \
+    -DDOWNLOAD_MINICONDA=TRUE -DMINICONDA_USE_PY3=TRUE \
+>&1 | tee  cmake.log
+# Env
+[hmeij@n100 ~]$ module load cuda/11.6
+[hmeij@n100 ~]$ echo $CUDA_HOME
+/usr/local/cuda
+[hmeij@n100 ~]$ 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
+# [FIXED} cmake error on conda install, set to FALSE
+# OS native python, install on n[100-101]
+-- Python version 3.9 -- OK
+-- Found PythonLibs: /usr/lib64/libpython3.9.so (found version "3.9.6")
+-- Checking for Python package numpy -- not found
+-- Checking for Python package scipy -- not found
+-- Checking for Python package matplotlib -- not found
+-- Checking for Python package setuptools -- found
+[END FIXED]
+# mpi & cuda FALSE builds serial
+./run_cmake
+make install
+# lots and lots of warnings
+# then
+source /share/apps/CENTOS8/ohpc/software/amber/20/amber.sh
+# on n100 now, parallel, set miniconda flags to FALSE
+-MPI=TRUE
+./run_cmake
+make install
+# on n100 just change cuda flag
+-CUDA=TRUE
+./run_cmake
+make install
+#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>
+==== Amber22 ====
+OpenHPC
+<code>
+# First **all the necessary packages ** (yum install...)
+  tar xvfj ../AmberTools22.tar.bz2
+  tar xvfj ../Amber22.tar.bz2
+  cd amber20_src/
+  cd build/
+  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 \
+>&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]]**

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