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--- cluster:214 [2022/08/02 14:25]
hmeij07 [Amber22]
+++ cluster:214 [2022/08/03 09:13]
hmeij07 [Amber22]
@@ Line 642: / Line 642: @@
 ==== Amber22 ====
-First establish a successfull run with the **run.rocky** script for Amber20 (listed above). Then change the module in your script.
+First establish a successful run with the **run.rocky** script for Amber20 (listed above). Then change the module in your script.
 <code>
@@ Line 648: / Line 648: @@
 module load amber/22
-# if the module does not show up in the output of
+# if the module does not show up in the output of your console
 module avail
-# treat your cache as out of date
+# treat your module cache as out of date
 module --ignore_cache avail
@@ Line 658: / Line 658: @@
 </code>
-Amber22 is somehow incompatible with CentOS/Rocky openmpi (yum install). Hence the latest version of openmpi was compiled and installed into $AMBERHOME. No need to set PATHs, just sure to source amber.sh in your script. (compile instructions below for me...)
+Amber22 is somehow incompatible with CentOS/Rocky openmpi (yum install). Hence the latest version of openmpi was compiled and installed into $AMBERHOME. No need to set PATHs, just be sure to source amber.sh in your script. (compile instructions below for me...)
 https://ambermd.org/InstCentOS.php\\
-"download a recent version of OpenMPI at open-mpi.org, untar the distribution in amber22_src/AmberTools/src, and execute in that directory the configure_openmpi script. (Do this after you have done a serial install, and have sourced the amber.sh script in the installation folder to create an AMBERHOME
+"download a recent version of OpenMPI at open-mpi.org, untar the distribution in amber22_src/AmberTools/src, and execute in that directory the configure_openmpi script. (Do this after you have done a serial install, and have sourced the amber.sh script in the installation folder to create an AMBERHOME)"
 <code>
@@ Line 667: / Line 667: @@
 [hmeij@n79 src]$ echo $AMBERHOME
 /share/apps/CENTOS7/amber/amber22
 [hmeij@n79 src]$ which mpirun mpicc
 /share/apps/CENTOS7/amber/amber22/bin/mpirun
@@ Line 673: / Line 674: @@
 </code>
-First establish a successfull run with the **run.centos7** script for Amber20 (listed above). Then change the  script like so.
+First establish a success full run with the **run.centos** script for Amber20 (listed above). Then edit the  script and apply these edits. We had to use a specific compatible ''gcc/g++'' version to make this work. Hardware is getting too old.
 <code>
 # comment out the 2 export lines pointing to openmpi
-# mpi is setup by sourcing the amber.sh file
+##export PATH=/share/apps/CENTOS7/openmpi/4.0.4/bin:$PATH
+##export LD_LIBRARY_PATH=/share/apps/CENTOS7/openmpi/4.0.4/lib:$LD_LIBRARY_PATH
+# additional gcc 6.5.0
+export PATH=/share/apps/CENTOS7/gcc/6.5.0/bin:$PATH
+export LD_LIBRARY_PATH=/share/apps/CENTOS7/gcc/6.5.0/lib64:$LD_LIBRARY_PATH
+# edit or add correct source line, which and ldd lines just for debugging
+###source /usr/local/amber16/amber.sh # works on mwgpu
+###source /usr/local/amber20/amber.sh # works on exx96
+source /share/apps/CENTOS7/amber/amber22/amber.sh # works on mwgpu and exx96
+which nvcc mpirun python
+ldd `which pmemd.cuda_SPFP`
 </code>

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