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cluster:213 [2022/07/25 09:31]
hmeij07 [Amber20]
cluster:213 [2022/07/25 14:52] (current)
hmeij07 [Amber22]
Line 342: Line 342:
 <code> <code>
  
-Fist **all the necessary packages ** (yum install...)+# First **all the necessary packages ** (yum install...)
  
  988  tar xvfj ../AmberTools22.tar.bz2   988  tar xvfj ../AmberTools22.tar.bz2 
Line 362: Line 362:
 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/ to n100:/usr/local/src/tmp/
  
-# Env 
  
-[hmeij@n100 ~]$ module load cuda/11.6+source /share/apps/CENTOS8/ohpc/software/amber/22/amber.sh 
 +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 gcc/gfortran 
-/usr/local/cuda/bin/nvcc +
-/opt/ohpc/pub/mpi/openmpi4-gnu9/4.1.1/bin/mpicc +
-/opt/ohpc/pub/compiler/gcc/9.4.0/bin/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: /usr/lib64/libpython3.9.so (found version "3.9.6" 
--- 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 
-./run_cmake +
-make install +
-# lots and lots of warnings +
- +
-# then +
-source /share/apps/CENTOS8/ohpc/software/amber/20/amber.sh +
- +
-# on n100 now, parallel, set miniconda flags to FALSE+
 -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
 +/opt/ohpc/pub/compiler/gcc/9.4.0/bin/gcc
 +/share/apps/CENTOS8/ohpc/software/amber/22/bin/mpicc
 +/usr/local/cuda/bin/nvcc
 +[hmeij@n100 ~]$ echo $CUDA_HOME
 +/usr/local/cuda
 +
 +-MPI=TRUE
 -CUDA=TRUE -CUDA=TRUE
 +-DDOWNLOAD_MINICONDA=FALSE
 ./run_cmake ./run_cmake
 make install make install
 +
 +
 +[hmeij@n100 ~]$ which nvcc mpicc gcc
 +/usr/local/cuda/bin/nvcc
 +/opt/ohpc/pub/mpi/openmpi4-gnu9/4.1.1/bin/mpicc
 +/opt/ohpc/pub/compiler/gcc/9.4.0/bin/gcc
  
 #tests #tests
Line 420: Line 423:
  
 </code> </code>
- 
-**[[cluster:0|Back]]** 
  
  
 **[[cluster:0|Back]]** **[[cluster:0|Back]]**
  
cluster/213.1658755918.txt.gz · Last modified: 2022/07/25 09:31 by hmeij07