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cluster:213 [2022/07/25 13:31] hmeij07 [Amber22] |
cluster:213 [2023/02/09 14:33] hmeij07 |
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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 | + | |
+ | cat / | ||
# fstab file mounts | # fstab file mounts | ||
+ | mkdir -p /zfshomes /home66 /home33 /mindstore / | ||
# 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 / | ||
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# check | # check | ||
chronyc sources | chronyc sources | ||
+ | |||
+ | # 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 " | ||
# 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! | ||
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# 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 " | ||
+ | |||
+ | yum install net-snmp-utils net-snmp-libs net-snmp net-snmp-agent-libs | ||
+ | |||
+ | # edit / | ||
+ | rocommunity public | ||
+ | dontLogTCPWrappersConnects yes | ||
+ | # enable, start, add to zenoss | ||
+ | |||
# compute nodes only | # compute nodes only | ||
Line 201: | Line 216: | ||
yum install dmtcp dmtcp-devel | yum install dmtcp dmtcp-devel | ||
- | # check status of service munge | + | |
yum clean all | yum clean all | ||
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# 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 244: | ||
scp cottontail2:/ | scp cottontail2:/ | ||
scp cottontail2:/ | scp cottontail2:/ | ||
+ | | ||
+ | # /etc/bashrc add | ||
+ | # ohpc lmod gcc mpicc | ||
+ | export PATH=/ | ||
+ | export LD_LIBRARY_PATH=/ | ||
+ | |||
| | ||
# / | # / | ||
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sleep 15 | sleep 15 | ||
/ | / | ||
+ | |||
+ | |||
+ | ## 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 * * * * / | ||
</ | </ | ||
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< | < | ||
+ | |||
+ | # First **all the necessary packages ** (yum install...) | ||
| | ||
Line 340: | Line 376: | ||
< | < | ||
- | Fist **all the necessary packages ** (yum install...) | + | # First **all the necessary packages ** (yum install...) |
| | ||
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make install | make install | ||
- | # Note | + | |
+ | # Note !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! | ||
The OpenMPI and MPICH system installations provided by CentOS | The OpenMPI and MPICH system installations provided by CentOS | ||
- | (i.e., through yum install) are known to be somehow incompatible with Amber22. | + | (i.e., through yum install) |
- | # OUCH | + | are known to be somehow incompatible with Amber22. |
+ | # OUCH !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! | ||
# GO TO node n100 | # GO TO node n100 | ||
+ | # copy head node's amber22_src/ | ||
- | # Env | ||
- | [hmeij@n100 ~]$ module load cuda/11.6 | + | source |
+ | echo $AMBERHOME | ||
- | [hmeij@n100 ~]$ echo $CUDA_HOME | + | # install latest openmpi version |
- | /usr/local/cuda | + | cd amber_src/Ambertools/src |
+ | tar xvfj ../../../../openmpi-4.1.4.tar.bz2 | ||
- | [hmeij@n100 ~]$ which nvcc mpicc gcc | + | ./configure_openmpi gnu # openhpc |
- | / | + | |
- | / | + | |
- | / | + | |
- | # [FIXED} cmake error on conda install, set to FALSE | ||
- | # OS native python, install on n[100-101] | ||
- | -- Python version 3.9 -- OK | ||
- | -- Found PythonLibs: / | ||
- | -- 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 | + | # on n100 now, parallel, set |
+ | -MPI=TRUE | ||
+ | -DDOWNLOAD_MINICONDA=FALSE | ||
./run_cmake | ./run_cmake | ||
make install | make install | ||
- | # lots and lots of warnings | ||
- | # then | + | # on n100 just change cuda flag |
- | source | + | |
+ | [hmeij@n100 build]$ module load cuda/11.6 | ||
+ | [hmeij@n100 build]$ which gcc mpicc nvcc | ||
+ | / | ||
+ | / | ||
+ | / | ||
+ | [hmeij@n100 ~]$ echo $CUDA_HOME | ||
+ | / | ||
- | # on n100 now, parallel, set miniconda flags to FALSE | ||
-MPI=TRUE | -MPI=TRUE | ||
- | ./run_cmake | ||
- | make install | ||
- | |||
- | # on n100 just change cuda flag | ||
-CUDA=TRUE | -CUDA=TRUE | ||
+ | -DDOWNLOAD_MINICONDA=FALSE | ||
./run_cmake | ./run_cmake | ||
make install | make install | ||
+ | |||
+ | |||
+ | [hmeij@n100 ~]$ which nvcc mpicc gcc | ||
+ | / | ||
+ | / | ||
+ | / | ||
#tests | #tests | ||
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</ | </ | ||
- | |||
- | **[[cluster: | ||
**[[cluster: | **[[cluster: | ||