Changes between Version 1 and Version 2 of cypress/glibc-version-problems

Timestamp:

06/09/23 13:43:08 (3 years ago)

Author:

fuji

Comment:

—

cypress/glibc-version-problems

@@ -10 +10 @@
 }}}
 
-Since glibc version on Centos version 6.5 nodes is 2.12, GLIBC_2.14 isn't available. It is possible to run this software if you use the compute nodes in partition '''centos7''', which have Centos version 7.4 with glibc version 2.17. See [https://wiki.hpc.tulane.edu/trac/wiki/cypress/using#SelectingCentOSglibcVersionViaSLURMpartition here] for more details.
+Since glibc version on Centos version 6.5 nodes is '''2.12''', '''GLIBC_2.14''' isn't available. It is possible to run this software if you use the compute nodes in partition '''centos7''', which have Centos version 7.4 with glibc version '''2.17'''. See [https://wiki.hpc.tulane.edu/trac/wiki/cypress/using#SelectingCentOSglibcVersionViaSLURMpartition here] for more details.
 
-See the alternate solution below if your software requires a glibc version greater than 2.17.
+See the alternate solution below if your software requires a glibc version greater than '''2.17'''.
 
 == Work with Singularity Images ==
-[https://sylabs.io/ Singularity] allows you to run an application built for a different distribution of Linux than Cypress OS (Centos 6 or 7). Here we run Rockylinux 9.2 on Cypress using Singularity.
+[https://sylabs.io/ Singularity] allows you to run an application built for a different distribution of Linux than Cypress OS (Centos 6 or 7). Here we run '''Rockylinux 9.2''' on Cypress using Singularity.
 
-=== Run Singularity Images Interactively ===
+=== Run Rockylinux Images Interactively ===
+Start an interactive session with '''centos7''' partition.
+{{{
+ idev -t 8 --partition=centos7
+}}}
+Load Singularity module.
+{{{
+ module load singularity/3.9.0
+}}}
+Setup the environmental variables
+{{{
+ source /lustre/project/singularity_images/setup_cypress.sh
+}}}
+Run bash shell in Rockylinux Images,
+{{{
+ singularity shell -s /bin/bash /lustre/project/singularity_images/rockylinux-9.2.sif
+}}}
+You will get a command line prompt. Now the glibc version is '''2.34'''.
+{{{
+Apptainer> ldd --version
+ldd (GNU libc) 2.34
+Copyright (C) 2021 Free Software Foundation, Inc.
+This is free software; see the source for copying conditions.  There is NO
+warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+Written by Roland McGrath and Ulrich Drepper.
+}}}
+
+You can use command line tools as you usually do on Centos6/7 nodes. '''module''' command also works but some of the modules may not work because of library incompatibility.
 
 
+=== Run Scripts on Rockylinux in Bachjob ===
+An example Slurm script.
+{{{
+#!/bin/bash
+#SBATCH --job-name=Singularity # Job Name
+#SBATCH --partition=centos7    # Partition must be centos7
+#SBATCH --qos=normal           # Quality of Service normal or long
+#SBATCH --time=0-01:00:00      # Wall clock time limit in Days-HH:MM:SS
+#SBATCH --nodes=1              # Node count required for the job
+#SBATCH --ntasks-per-node=1    # Number of tasks to be launched per Node
+#SBATCH --cpus-per-task=1     # Number of threads per task (OMP threads 1-20)
 
+# Load Singularity module
+module load singularity/3.9.0
+
+# Setup the environmental variables 
+SingularityImageDir=/lustre/project/singularity_images
+source $SingularityImageDir/setup_cypress.sh
+
+# Run a command on RockyLinux 
+singularity exec $SingularityImageDir/rockylinux-9.2.sif gcc --version
+}}}
+The example above runs gcc --version on RockyLinux. Submitting job is the same as you usually do. (See [https://wiki.hpc.tulane.edu/trac/wiki/cypress/using#IntroductiontoManagedClusterComputing here].) 
+When the job is finished, the log file should contain the output from gcc --version command, which will be:
+{{{
+gcc (GCC) 11.3.1 20221121 (Red Hat 11.3.1-4)
+Copyright (C) 2021 Free Software Foundation, Inc.
+This is free software; see the source for copying conditions.  There is NO
+warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+}}}
+
+
+If you want to run a bash script, assuming 'my_script.sh' is in the current working directory, modify the above as
+{{{
+singularity run $SingularityImageDir/rockylinux-9.2.sif /bin/bash -l -c ./my_script.sh
+}}}
+
+'my_script.sh' must be executable. You can make it by 'chmod' command (See [https://wiki.hpc.tulane.edu/trac/wiki/cypress/BasicLinuxComands#chmod here].)
+{{{
+chmod u+x my_script.sh
+}}}
+
+For example, 'my_script.sh' is 
+{{{
+#!/bin/bash
+module load intel-psxe/2016
+echo "Hello world from $0 running in ${SINGULARITY_NAME}"
+pwd
+date
+icc --version
+}}}
+When the job is finished, the log file will have:
+{{{
+Hello world from ./my_script.sh running in rockylinux-9.2.sif
+/home/userid/test
+Fri Jun  9 13:21:01 CDT 2023
+icc (ICC) 16.0.0 20150815
+Copyright (C) 1985-2015 Intel Corporation.  All rights reserved.
+}}}
+
+If you find missing packages in rockylinux-9.2.sif, please let us know.