Warning: Undefined array key "DOKU_PREFS" in /usr/share/dokuwiki/inc/common.php on line 2082
cluster:213 [DokuWiki]

DokuWiki

User Tools

Site Tools

Trace:
cluster:213

Differences

This shows you the differences between two versions of the page.

Link to this comparison view

Both sides previous revision Previous revision
Next revision 		Previous revision
Next revision Both sides next revision
cluster:213 [2022/07/25 11:10]
hmeij07 [Amber22] 		cluster:213 [2023/01/31 14:25]
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)
  
Line 94: Line 86:
 ## 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
  
-# 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 113:
 # 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 170:
 # 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 243: Line 260:
  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 373: Line 388:
  
 # copy head node's amber22_src/ to n100:/usr/local/src/tmp/ # 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 # install latest openmpi version
Line 378: Line 397:
 tar xvfj ../../../../openmpi-4.1.4.tar.bz2  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
  
-# Env+-MPI=TRUE 
 +-CUDA=TRUE 
 +-DDOWNLOAD_MINICONDA=FALSE 
 +./run_cmake 
 +make install
  
-[hmeij@n100 ~]$ module load cuda/11.6 
- 
-[hmeij@n100 ~]$ echo $CUDA_HOME 
-/usr/local/cuda 
  
 [hmeij@n100 ~]$ which nvcc mpicc gcc [hmeij@n100 ~]$ which nvcc mpicc gcc
Line 394: Line 427:
 /opt/ohpc/pub/mpi/openmpi4-gnu9/4.1.1/bin/mpicc /opt/ohpc/pub/mpi/openmpi4-gnu9/4.1.1/bin/mpicc
 /opt/ohpc/pub/compiler/gcc/9.4.0/bin/gcc /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 #tests
cluster/213.txt · Last modified: 2024/01/12 10:09 by hmeij07

Page Tools

Except where otherwise noted, content on this wiki is licensed under the following license: CC Attribution-Share Alike 4.0 International
CC Attribution-Share Alike 4.0 International Donate Powered by PHP Valid HTML5 Valid CSS Driven by DokuWiki