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cluster:213 [2022/05/12 13:11] hmeij07 |
cluster:213 [2023/02/14 14:09] hmeij07 |
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cd / | cd / | ||
vi ifcfg-eth0 # 192.168.102.x | vi ifcfg-eth0 # 192.168.102.x | ||
- | vi ifcfg-eth1 # 10.10.102.x | + | vi ifcfg-eth1 # 10.10.102.x |
vi ifcfg-eth3 # 129.133.52.x | vi ifcfg-eth3 # 129.133.52.x | ||
+ | scp 192.168.102.112:/ | ||
+ | |||
systemctl restart network | systemctl restart network | ||
ping -c 3 192.168.102.42 | ping -c 3 192.168.102.42 | ||
Line 64: | Line 66: | ||
systemctl start iptables # and enable | systemctl start iptables # and enable | ||
iptables -L | iptables -L | ||
- | systemctl stop firewalld | ||
- | systemctl disable firewalld | ||
Line 73: | Line 73: | ||
iptables -L # check! | iptables -L # check! | ||
- | # Rocky8 | + | |
- | # https:// | + | |
- | 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 " | + | |
# other configs | # other configs | ||
vi / | vi / | ||
mv /home /usr/local/ | mv /home /usr/local/ | ||
+ | cd /;ln -s / | ||
+ | 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 / | ||
- | ## cottontail2 = greentail52 sections | ||
+ | #exx96 | ||
mkdir /sanscratch / | mkdir /sanscratch / | ||
chmod ugo+rwx /sanscratch / | chmod ugo+rwx /sanscratch / | ||
chmod o+t /sanscratch / | chmod o+t /sanscratch / | ||
+ | # 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 / | ln -s / | ||
ln -s / | ln -s / | ||
ln -s / | ln -s / | ||
- | ln -s /zfshomes | + | ls -l |
+ | |||
+ | cat / | ||
# fstab file mounts | # fstab file mounts | ||
+ | mkdir -p /zfshomes /home66 /home33 /mindstore / | ||
+ | mkdir -p / | ||
# cottontail2 = greentail52 | # cottontail2 = greentail52 | ||
# n100-n101 = n79 | # n100-n101 = n79 | ||
- | # postfix | ||
- | dnf install postfix | ||
- | dnf install mailx | ||
- | systemctl enable postfix | ||
- | echo " | ||
# on head node / | # on head node / | ||
Line 122: | Line 112: | ||
Server 192.168.102.251 | Server 192.168.102.251 | ||
# check | # check | ||
+ | systemctl restart chronyd | ||
chronyc sources | chronyc sources | ||
+ | |||
+ | # Rocky8 | ||
+ | # https:// | ||
+ | dnf config-manager --set-enabled powertools -y | ||
+ | dnf install epel-release -y | ||
+ | dnf install netcdf netcdf-devel -y | ||
+ | dnf install yum-utils # yumdownloader -y | ||
+ | dnf install ddd grace gnuplot alpine -y # pico | ||
+ | |||
+ | yum groupinstall " | ||
# on head node install from epel repo | # on head node install from epel repo | ||
- | yum install slurm-openlava | + | ### yum install slurm-openlava |
# error on conflicting libs, too bad! | # error on conflicting libs, too bad! | ||
Line 133: | Line 134: | ||
yum install epel-release -y | yum install epel-release -y | ||
yum install flex bison -y | yum install flex bison -y | ||
- | yum install tcl tcl-devel dmtcp -y | + | yum install tcl tcl-devel |
yum install net-snmp net-snmp-libs net-tools net-snmp-utils -y | yum install net-snmp net-snmp-libs net-tools net-snmp-utils -y | ||
yum install freeglut-devel libXi-devel libXmu-devel -y | yum install freeglut-devel libXi-devel libXmu-devel -y | ||
Line 168: | Line 169: | ||
# 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 " | ||
+ | |||
+ | |||
+ | # edit / | ||
+ | rocommunity public | ||
+ | dontLogTCPWrappersConnects yes | ||
+ | # enable, start, add to zenoss | ||
+ | |||
# compute nodes only | # compute nodes only | ||
Line 198: | Line 213: | ||
# obabel chem file formats | # obabel chem file formats | ||
yum install openbabel openbabel-devel | yum install openbabel openbabel-devel | ||
- | # dmtcp | ||
- | yum install dmtcp dmtcp-devel | ||
- | # check status of service munge | + | |
yum clean all | yum clean all | ||
# eth3 onboot=no, private networks only | # eth3 onboot=no, private networks only | ||
systemctl disable iptables | systemctl disable iptables | ||
- | reboot | + | |
# now make it an ohpc compute node | # now make it an ohpc compute node | ||
yum repolist | yum repolist | ||
- | yum install ohpc-base-compute | + | |
+ | | ||
| | ||
scp cottontail2:/ | scp cottontail2:/ | ||
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 227: | Line 243: | ||
scp cottontail2:/ | scp cottontail2:/ | ||
scp cottontail2:/ | scp cottontail2:/ | ||
+ | | ||
+ | # /etc/bashrc add | ||
+ | # ohpc lmod gcc mpicc | ||
+ | export PATH=/ | ||
+ | export LD_LIBRARY_PATH=/ | ||
+ | |||
| | ||
# / | # / | ||
Line 234: | Line 256: | ||
/ | / | ||
| | ||
- | # start via rc.local | + | # start via rc.local |
- | chmod +x / | + | #chmod +x / |
#timing issue with munge | #timing issue with munge | ||
- | sleep 15 | + | #sleep 15 |
- | / | + | #/ |
+ | |||
+ | systemctl stop firewalld | ||
+ | systemctl disable firewalld | ||
+ | |||
+ | |||
+ | ## edit passwd, shadow, group, hosts files ## | ||
+ | ## make -orig backups and stage in / | ||
+ | ## cottontail2 = greentail52 sections | ||
| | ||
# slurmd ??? | # slurmd ??? | ||
libhwloc.so.15 => / | libhwloc.so.15 => / | ||
- | # add to zenoss edit /etc/snmp/snmpd.conf, enable and start | + | # crontab |
- | rocommunity public | + | |
- | dontLogTCPWrappersConnects yes | + | # ionice gaussian |
+ | 0,15,30,45 * * * * /share/apps/scripts/ | ||
+ | |||
+ | # cpu temps | ||
+ | 40 * * * * / | ||
+ | |||
+ | # file date_ctt2.sh | ||
+ | |||
+ | # ctt /etc/pdsh | ||
+ | |||
+ | # ctt:/ | ||
</ | </ | ||
Line 266: | Line 307: | ||
< | < | ||
+ | |||
+ | # First **all the necessary packages ** (yum install...) | ||
| | ||
Line 275: | Line 318: | ||
# 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 |
cmake $AMBER_PREFIX/ | cmake $AMBER_PREFIX/ | ||
-DCMAKE_INSTALL_PREFIX=/ | -DCMAKE_INSTALL_PREFIX=/ | ||
Line 333: | Line 376: | ||
</ | </ | ||
+ | |||
+ | ==== Amber22 ==== | ||
+ | |||
+ | OpenHPC | ||
+ | |||
+ | < | ||
+ | |||
+ | # First **all the necessary packages ** (yum install...) | ||
+ | |||
+ | | ||
+ | 989 tar xvfj ../ | ||
+ | 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/ | ||
+ | -DCMAKE_INSTALL_PREFIX=/ | ||
+ | -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/ | ||
+ | |||
+ | |||
+ | source / | ||
+ | echo $AMBERHOME | ||
+ | |||
+ | # install latest openmpi version | ||
+ | cd amber_src/ | ||
+ | tar xvfj ../ | ||
+ | |||
+ | ./ | ||
+ | |||
+ | |||
+ | # on n100 now, parallel, set | ||
+ | -MPI=TRUE | ||
+ | -DDOWNLOAD_MINICONDA=FALSE | ||
+ | ./run_cmake | ||
+ | make install | ||
+ | |||
+ | # on n100 just change cuda flag | ||
+ | |||
+ | [hmeij@n100 build]$ module load cuda/11.6 | ||
+ | [hmeij@n100 build]$ which gcc mpicc nvcc | ||
+ | / | ||
+ | / | ||
+ | / | ||
+ | [hmeij@n100 ~]$ echo $CUDA_HOME | ||
+ | / | ||
+ | |||
+ | -MPI=TRUE | ||
+ | -CUDA=TRUE | ||
+ | -DDOWNLOAD_MINICONDA=FALSE | ||
+ | ./run_cmake | ||
+ | make install | ||
+ | |||
+ | |||
+ | [hmeij@n100 ~]$ which nvcc mpicc gcc | ||
+ | / | ||
+ | / | ||
+ | / | ||
+ | |||
+ | #tests | ||
+ | cd $AMBERHOME | ||
+ | make test.serial | ||
+ | export DO_PARALLEL=" | ||
+ | make test.parallel | ||
+ | export CUDA_VISIBLE_DEVICES=0 | ||
+ | make test.cuda.serial | ||
+ | make test.cuda.parallel | ||
+ | |||
+ | </ | ||
+ | |||
**[[cluster: | **[[cluster: | ||