Differences

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--- cluster:214 [2022/08/02 13:38] – [Amber22] hmeij07
+++ cluster:214 [2023/08/18 16:19] (current) – [Upgrading] hmeij07
@@ Line 397: / Line 397: @@
 ==== Upgrading ====
-Figure out an upgrade process before going production (don't forget any chroot images and rebuild images).
+Figure out an upgrade process before going production.
+  * **Do you actually want to upgrade OpenHPC?**
+    * v2.6 deploys ww4.x (maybe not want this, containers)
+    * chroot images and rebuild images running rocky 8
+    * OneAPI similar conflicts? (/opt/intel and /opt/ohpc/pub)
+    * slurm complications?
+  * **Upgrade Openhpc, OneAPI should be on new head node**
+    * test compatibility compilers
+    * slurm clients
 <code>
@@ Line 403: / Line 412: @@
 yum upgrade "*-ohpc"
 yum upgrade "ohpc-base"
+or
+yum update --disablerepo=* --enablerepo=[oneAPI,OpenHPC]
 </code>
+**Upgrade history**
+  * OS only, 30 Jun 2022 (90+ days up) - no ohpc, oneapi (/opt)
+  * OS only, 18 Aug 2023 (440+ days up) - no ohpc, oneapi (/opt)
+  *
 ==== example modules ====
@@ Line 460: / Line 477: @@
 Amber cmake download fails with READLINE error ... package readline-devel needs to be installed to get past that which pulls in   ncurses-c++-libs-6.1-9.20180224.el8.x86_64   ncurses-devel-6.1-9.20180224.el8.x86_64   readline-devel-7.0-10.el8.x86_64
-** Example script run.rocky for cpu or gpu run** (not for queues mwgpu, exx96)
+** Example script run.rocky for cpu or gpu run** (for queues amber128 [n78] and test [n100-n101] for gpus and mw128 and tinymem for cpus)
 <code>
@@ Line 531: / Line 548: @@
 </code>
-** Example script run.centos for cpui or gpu run** (queues mwgpu, exx96)
+** Example script run.centos for cpus or gpu run** (queues mwgpu, exx96)
 <code>
@@ Line 642: / Line 659: @@
 ==== Amber22 ====
-First establish a successfull run with the ''run.rocky'' script for Amber20 (listed above). Then change the module in your script.
+Amber22 is somehow incompatible with CentOS/Rocky openmpi (yum install). Hence the latest version of openmpi was compiled and installed into $AMBERHOME. No need to set PATHs, just be sure to source amber.sh in your script. (compile instructions below for me...)
+https://ambermd.org/InstCentOS.php\\
+"download a recent version of OpenMPI at open-mpi.org, untar the distribution in amber22_src/AmberTools/src, and execute in that directory the configure_openmpi script. (Do this after you have done a serial install, and have sourced the amber.sh script in the installation folder to create an AMBERHOME)"
+<code>
+[hmeij@n79 src]$ echo $AMBERHOME
+/share/apps/CENTOS7/amber/amber22
+[hmeij@n79 src]$ which mpirun mpicc
+/share/apps/CENTOS7/amber/amber22/bin/mpirun
+/share/apps/CENTOS7/amber/amber22/bin/mpicc
+</code>
+First establish a successful run with the **run.rocky** script for Amber20 (listed above). Then change the module in your script. (for queues amber128 [n78] and test [n100-n101] for gpus and mw128 and tinymem for cpus)
 <code>
@@ Line 648: / Line 681: @@
 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 691: @@
 </code>
-Amber22 is somehow incompatible with CentOS/Rocky openmpi (yum install). Hence the latest version of openmpi was compiled and installed into $AMBERHOME. No need to set PATHs, just sure to source amber.sh in your script. (compile instructions below for me...)
+First establish a success full run with the **run.centos** script for Amber20 (listed above, for cpus or gpus on queues mwgpu and exx96).
-https://ambermd.org/InstCentOS.php\\
+Then edit the  script and apply these edits. We had to use a specific compatible ''gcc/g++'' version to make this work. Hardware is getting too old.
-"download a recent version of OpenMPI at open-mpi.org, untar the distribution in amber22_src/AmberTools/src, and execute in that directory the configure_openmpi script. (Do this after you have done a serial install, and have sourced the amber.sh script in the installation folder to create an AMBERHOME
+<code>
+# comment out the 2 export lines pointing to openmpi
+##export PATH=/share/apps/CENTOS7/openmpi/4.0.4/bin:$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>
 \\