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cluster:213 [2022/05/10 17:48] hmeij07 |
cluster:213 [2022/07/25 13:31] hmeij07 [Amber20] |
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#easybuild | #easybuild | ||
- | yum install | + | yum install |
# amber20 cmake readline error fix needs | # amber20 cmake readline error fix needs | ||
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# 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 | ||
Line 198: | Line 200: | ||
# dmtcp | # dmtcp | ||
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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scp cottontail2:/ | scp cottontail2:/ | ||
scp cottontail2:/ | scp cottontail2:/ | ||
+ | scp cottontail2:/ | ||
+ | | ||
+ | # / | ||
+ | / | ||
+ | |||
#test | #test | ||
/ | / | ||
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< | < | ||
+ | |||
+ | # First **all the necessary packages ** (yum install...) | ||
| | ||
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# 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=/ | ||
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</ | </ | ||
+ | |||
+ | ==== Amber22 ==== | ||
+ | |||
+ | OpenHPC | ||
+ | |||
+ | < | ||
+ | |||
+ | Fist **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 $AMBER_PREFIX/ | ||
+ | -DCMAKE_INSTALL_PREFIX=/ | ||
+ | -DCOMPILER=GNU | ||
+ | -DMPI=FALSE -DCUDA=FALSE -DINSTALL_TESTS=TRUE \ | ||
+ | -DDOWNLOAD_MINICONDA=TRUE \ | ||
+ | 2>&1 | tee cmake.log | ||
+ | ./run_cmake | ||
+ | make install | ||
+ | |||
+ | # Note | ||
+ | The OpenMPI and MPICH system installations provided by CentOS | ||
+ | (i.e., through yum install) are known to be somehow incompatible with Amber22. | ||
+ | # OUCH | ||
+ | |||
+ | # GO TO node n100 | ||
+ | |||
+ | |||
+ | # Env | ||
+ | |||
+ | [hmeij@n100 ~]$ module load cuda/11.6 | ||
+ | |||
+ | [hmeij@n100 ~]$ echo $CUDA_HOME | ||
+ | / | ||
+ | |||
+ | [hmeij@n100 ~]$ which nvcc mpicc gcc | ||
+ | / | ||
+ | / | ||
+ | / | ||
+ | |||
+ | # [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 | ||
+ | ./run_cmake | ||
+ | make install | ||
+ | # lots and lots of warnings | ||
+ | |||
+ | # then | ||
+ | source / | ||
+ | |||
+ | # on n100 now, parallel, set miniconda flags to FALSE | ||
+ | -MPI=TRUE | ||
+ | ./run_cmake | ||
+ | make install | ||
+ | |||
+ | # on n100 just change cuda flag | ||
+ | -CUDA=TRUE | ||
+ | ./run_cmake | ||
+ | make install | ||
+ | |||
+ | #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: | **[[cluster: | ||