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cluster:213 [2022/07/25 13:19] hmeij07 [Amber20] |
cluster:213 [2023/01/31 19:19] hmeij07 |
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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) | ||
Line 94: | Line 96: | ||
## cottontail2 = greentail52 sections | ## 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 /share | + | |
# 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 | + | # add to zenoss edit /etc/snmp/snmpd.conf, enable and start |
- | dnf install mailx | + | rocommunity public |
- | systemctl enable postfix | + | dontLogTCPWrappersConnects yes |
- | echo " | + | |
# on head node / | # on head node / | ||
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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 " | ||
# compute nodes only | # compute nodes only | ||
Line 243: | Line 255: | ||
libhwloc.so.15 => / | libhwloc.so.15 => / | ||
- | # add to zenoss edit / | + | |
- | rocommunity public | + | |
- | dontLogTCPWrappersConnects yes | + | |
</ | </ | ||
Line 266: | Line 276: | ||
< | < | ||
+ | |||
+ | # First **all the necessary packages ** (yum install...) | ||
| | ||
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< | < | ||
+ | |||
+ | # First **all the necessary packages ** (yum install...) | ||
| | ||
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-DDOWNLOAD_MINICONDA=TRUE \ | -DDOWNLOAD_MINICONDA=TRUE \ | ||
2>&1 | tee cmake.log | 2>&1 | tee cmake.log | ||
+ | ./run_cmake | ||
+ | make install | ||
- | # Env | + | # Note !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! |
+ | The OpenMPI and MPICH system installations provided by CentOS | ||
+ | (i.e., through yum install) | ||
+ | are known to be somehow incompatible with Amber22. | ||
+ | # OUCH !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! | ||
- | [hmeij@n100 ~]$ module load cuda/11.6 | ||
- | [hmeij@n100 ~]$ echo $CUDA_HOME | + | # GO TO node n100 |
- | / | + | |
- | [hmeij@n100 ~]$ which nvcc mpicc gcc | + | # copy head node's amber22_src/ |
- | /usr/local/cuda/ | + | |
- | / | + | |
- | / | + | |
- | # [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 | + | source / |
- | ./run_cmake | + | echo $AMBERHOME |
- | make install | + | |
- | # lots and lots of warnings | + | # install latest openmpi version |
+ | cd amber_src/ | ||
+ | tar xvfj ../../ | ||
+ | |||
+ | ./ | ||
- | # then | ||
- | source / | ||
- | # on n100 now, parallel, set miniconda flags to FALSE | + | # on n100 now, parallel, set |
-MPI=TRUE | -MPI=TRUE | ||
+ | -DDOWNLOAD_MINICONDA=FALSE | ||
./run_cmake | ./run_cmake | ||
make install | make install | ||
# on n100 just change cuda flag | # on n100 just change cuda flag | ||
+ | |||
+ | [hmeij@n100 build]$ module load cuda/11.6 | ||
+ | [hmeij@n100 build]$ which gcc mpicc nvcc | ||
+ | / | ||
+ | / | ||
+ | / | ||
+ | [hmeij@n100 ~]$ echo $CUDA_HOME | ||
+ | / | ||
+ | |||
+ | -MPI=TRUE | ||
-CUDA=TRUE | -CUDA=TRUE | ||
+ | -DDOWNLOAD_MINICONDA=FALSE | ||
./run_cmake | ./run_cmake | ||
make install | make install | ||
+ | |||
+ | |||
+ | [hmeij@n100 ~]$ which nvcc mpicc gcc | ||
+ | / | ||
+ | / | ||
+ | / | ||
#tests | #tests | ||
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</ | </ | ||
- | |||
- | **[[cluster: | ||
**[[cluster: | **[[cluster: | ||