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--- cluster:213 [2022/05/10 14:03]
hmeij07
+++ cluster:213 [2022/07/25 14:18]
hmeij07 [Amber22]
@@ Line 185: / Line 185: @@
 # openjdk version "1.8.0_322"
 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
 yum install python39 python39-devel
@@ Line 198: / Line 200: @@
 # dmtcp
 yum install dmtcp dmtcp-devel
+# check status of service munge
 yum clean all
@@ Line 222: / Line 226: @@
   scp cottontail2:/etc/slurm/slurm.conf /etc/slurm/slurm.conf
   scp cottontail2:/etc/slurm/gres.conf /etc/slurm/gres.conf
+  scp cottontail2:/etc/profile.d/lmod.sh /etc/profile.d/
+# /var/[log|spool|run] need to be removed from
+/usr/libexec/warewulf/wwmkchroot/gold-template
 #test
   /usr/sbin/slurmd -D
@@ Line 257: / Line 266: @@
 <code>
+# First **all the necessary packages ** (yum install...)
   tar xvfj ../AmberTools21.tar.bz2
@@ Line 266: / Line 277: @@
 #  Assume this is Linux:
-# serial, do on heasd node, pull down miniconda, compile, install
+# serial, do on head node, with miniconda true, compile, install
   cmake $AMBER_PREFIX/amber20_src \
     -DCMAKE_INSTALL_PREFIX=/share/apps/CENTOS8/ohpc/software/amber/20 \
@@ Line 324: / Line 335: @@
 </code>
+==== Amber22 ====
+OpenHPC
+<code>
+# First **all the necessary packages ** (yum install...)
+  tar xvfj ../AmberTools22.tar.bz2
+  tar xvfj ../Amber22.tar.bz2
+  cd amber20_src/
+  cd build/
+  vi run_cmake
+#  Assume this is Linux:
+# serial, do on head node, with miniconda true, compile, install
+  cmake $AMBER_PREFIX/amber22_src \
+    -DCMAKE_INSTALL_PREFIX=/share/apps/CENTOS8/ohpc/software/amber/22 \
+    -DCOMPILER=GNU  \
+    -DMPI=FALSE -DCUDA=FALSE -DINSTALL_TESTS=TRUE \
+    -DDOWNLOAD_MINICONDA=TRUE \
+>&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
+# copy head node's amber22_src/ to n100:/usr/local/src/tmp/
+source /share/apps/CENTOS8/ohpc/software/amber/22/amber.sh
+echo $AMBERHOME
+# install latest openmpi version
+cd amber_src/Ambertools/src
+tar xvfj ../../../../openmpi-4.1.4.tar.bz2
+./configure_openmpi gnu # openhpc gcc/gfortran
+# on n100 now, parallel, set
+-MPI=TRUE
+-DDOWNLOAD_MINICONDA=FALSE
+./run_cmake
+make install
+# on n100 just change cuda flag
+module load cuda/11.6
+-MPI=TRUE
+-CUDA=TRUE
+-DDOWNLOAD_MINICONDA=FALSE
+./run_cmake
+make install
+[hmeij@n100 ~]$ echo $CUDA_HOME
+/usr/local/cuda
+[hmeij@n100 ~]$ 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
+cd $AMBERHOME
+make test.serial
+export DO_PARALLEL="mpirun -np 6"
+make test.parallel
+export CUDA_VISIBLE_DEVICES=0
+make test.cuda.serial
+make test.cuda.parallel
+</code>
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