cluster:213
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cluster:213 [2022/07/25 09:31] hmeij07 [Amber20] |
cluster:213 [2023/01/31 13:57] hmeij07 |
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| Line 88: | Line 88: | ||
| 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 $HOME) | ||
| Line 94: | Line 96: | ||
| ## cottontail2 = greentail52 sections | ## cottontail2 = greentail52 sections | ||
| + | #exx96 | ||
| mkdir /sanscratch / | mkdir /sanscratch / | ||
| chmod ugo+rwx /sanscratch / | chmod ugo+rwx /sanscratch / | ||
| chmod o+t /sanscratch / | chmod o+t /sanscratch / | ||
| + | # exx96 | ||
| # link localscratch in 1.4T /home to / | # link localscratch in 1.4T /home to / | ||
| - | mkdir /home | + | |
| - | cd /home # local dir | + | cd /home |
| ln -s / | ln -s / | ||
| ln -s / | ln -s / | ||
| ln -s / | ln -s / | ||
| - | ln -s /zfshomes /share | + | |
| # fstab file mounts | # fstab file mounts | ||
| + | mkdir -p /zfshomes /home66 /home33 /mindstore / | ||
| # cottontail2 = greentail52 | # cottontail2 = greentail52 | ||
| # n100-n101 = n79 | # n100-n101 = n79 | ||
| Line 342: | Line 347: | ||
| < | < | ||
| - | Fist **all the necessary packages ** (yum install...) | + | # First **all the necessary packages ** (yum install...) |
| | | ||
| Line 362: | Line 367: | ||
| make install | make install | ||
| - | # Note | + | |
| + | # Note !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! | ||
| The OpenMPI and MPICH system installations provided by CentOS | The OpenMPI and MPICH system installations provided by CentOS | ||
| - | (i.e., through yum install) are known to be somehow incompatible with Amber22. | + | (i.e., through yum install) |
| - | # OUCH | + | are known to be somehow incompatible with Amber22. |
| + | # OUCH !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! | ||
| # GO TO node n100 | # GO TO node n100 | ||
| + | # copy head node's amber22_src/ | ||
| - | # Env | ||
| - | [hmeij@n100 ~]$ 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 | ||
| Line 420: | Line 428: | ||
| </ | </ | ||
| - | |||
| - | **[[cluster: | ||
| **[[cluster: | **[[cluster: | ||
cluster/213.txt · Last modified: 2024/01/12 10:09 by hmeij07
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