This shows you the differences between two versions of the page.
Both sides previous revision Previous revision Next revision | Previous revision Last revision Both sides next revision | ||
cluster:213 [2022/04/06 13:31] hmeij07 [Pics] |
cluster:213 [2024/01/10 20:28] hmeij07 |
||
---|---|---|---|
Line 44: | Line 44: | ||
# Put the warewulf cluster key in authorized_keys | # Put the warewulf cluster key in authorized_keys | ||
+ | # Put eth0 fingerprints in cottontail/ | ||
+ | # add to relevant known_hosts_servername file | ||
# configure private subnets and ping file server | # configure private subnets and ping file server | ||
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 62: | Line 66: | ||
systemctl start iptables # and enable | systemctl start iptables # and enable | ||
iptables -L | iptables -L | ||
- | systemctl stop firewalld | ||
- | systemctl disable firewalld | ||
Line 71: | 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 | + | |
# 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 / | ||
- | allow 192.168.0.0/ | + | allow 192.168.0.0/ |
# compute nodes / | # compute nodes / | ||
#pool 2.pool.ntp.org iburst | #pool 2.pool.ntp.org iburst | ||
Line 119: | 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 130: | 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 139: | Line 143: | ||
yum install cmake -y | yum install cmake -y | ||
yum install libjpeg libjpeg-devel libjpeg-turbo-devel -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 \ | yum -y install tcsh make \ | ||
gcc gcc-gfortran gcc-c++ \ | gcc gcc-gfortran gcc-c++ \ | ||
Line 156: | 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 173: | Line 200: | ||
# openjdk version " | # openjdk version " | ||
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 | ||
+ | ln -s / | ||
# fftw 3.3.5-11.el8 | # fftw 3.3.5-11.el8 | ||
yum install fftw fftw-devel | yum install fftw fftw-devel | ||
Line 183: | 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 | + | |
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 | + | |
+ | yum install singularity-ohpc | ||
+ | | ||
| | ||
scp cottontail2:/ | scp cottontail2:/ | ||
yum install ohpc-slurm-client | yum install ohpc-slurm-client | ||
+ | # check status of service munge | ||
+ | rpm -ivh / | ||
systemctl enable munge | systemctl enable munge | ||
systemctl start munge | systemctl start munge | ||
Line 209: | Line 244: | ||
scp cottontail2:/ | scp cottontail2:/ | ||
scp cottontail2:/ | scp cottontail2:/ | ||
+ | scp cottontail2:/ | ||
+ | | ||
+ | # /etc/bashrc add | ||
+ | # ohpc lmod gcc mpicc | ||
+ | export PATH=/ | ||
+ | export LD_LIBRARY_PATH=/ | ||
+ | |||
+ | | ||
+ | # / | ||
+ | / | ||
+ | |||
#test | #test | ||
/ | / | ||
| | ||
- | # 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 | ||
+ | |||
+ | systemctl | ||
+ | systemctl stop dnf-makecache.timer | ||
+ | |||
+ | mv / | ||
+ | mv / | ||
+ | |||
+ | |||
+ | ## edit passwd, shadow, group, hosts files ## | ||
+ | ## make -orig backups and stage in / | ||
+ | ## cottontail2 = greentail52 sections | ||
+ | chown -R munge:munge /etc/munge / | ||
+ | chown -R slurm:munge / | ||
+ | |||
| | ||
# 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 * * * * / | ||
+ | |||
+ | # cpu temps | ||
+ | 40 * * * * / | ||
+ | |||
+ | on compute node /etc/security/limits.conf | ||
+ | * - | ||
+ | |||
+ | |||
+ | # file date_ctt2.sh | ||
+ | |||
+ | # ctt /etc/pdsh | ||
+ | |||
+ | # ctt:/ | ||
+ | |||
+ | # ctt2:/ | ||
</ | </ | ||
Line 244: | Line 324: | ||
< | < | ||
+ | |||
+ | # First **all the necessary packages ** (yum install...) | ||
| | ||
Line 253: | Line 335: | ||
# Assume this is Linux: | # Assume this is Linux: | ||
+ | # serial, do on head node, with miniconda true, compile, install | ||
cmake $AMBER_PREFIX/ | cmake $AMBER_PREFIX/ | ||
- | -DCMAKE_INSTALL_PREFIX=/ | + | -DCMAKE_INSTALL_PREFIX=/ |
-DCOMPILER=GNU | -DCOMPILER=GNU | ||
- | -DMPI=TRUE -DCUDA=TRUE -DINSTALL_TESTS=TRUE \ | + | -DMPI=FALSE -DCUDA=FALSE -DINSTALL_TESTS=TRUE \ |
-DDOWNLOAD_MINICONDA=TRUE -DMINICONDA_USE_PY3=TRUE \ | -DDOWNLOAD_MINICONDA=TRUE -DMINICONDA_USE_PY3=TRUE \ | ||
2>&1 | tee cmake.log | 2>&1 | tee cmake.log | ||
Line 272: | Line 355: | ||
/ | / | ||
- | # cmake error on conda install, set to FALSE | + | # [FIXED} |
# OS native python, install on n[100-101] | # OS native python, install on n[100-101] | ||
-- Python version 3.9 -- OK | -- Python version 3.9 -- OK | ||
Line 281: | Line 363: | ||
-- Checking for Python package matplotlib -- not found | -- Checking for Python package matplotlib -- not found | ||
-- Checking for Python package setuptools -- found | -- Checking for Python package setuptools -- found | ||
+ | [END FIXED] | ||
- | # mpi, cuda FALSE builds serial | + | # mpi & cuda FALSE builds serial |
- | # I happened to do them at the same time | + | ./run_cmake |
make install | make install | ||
# lots and lots of warnings | # lots and lots of warnings | ||
- | source / | + | # then |
+ | source / | ||
- | cd $AMBERHOME/ | + | # on n100 now, parallel, set miniconda flags to FALSE |
- | ./ | + | |
-MPI=TRUE | -MPI=TRUE | ||
+ | ./run_cmake | ||
make install | make install | ||
- | # then | + | # on n100 just change cuda flag |
-CUDA=TRUE | -CUDA=TRUE | ||
+ | ./run_cmake | ||
make install | make install | ||
+ | #tests | ||
+ | cd $AMBERHOME | ||
+ | make test.serial | ||
export DO_PARALLEL=" | export DO_PARALLEL=" | ||
make test.parallel | make test.parallel | ||
Line 305: | Line 393: | ||
</ | </ | ||
+ | |||
+ | ==== 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: | ||