Merge pull request #206 from xylar/update-chrysalis

Update netcdf-c and netcdf-fortran on chrysalis
E3SM-Project · Oct 26, 2024 · b78eb1d · b78eb1d
2 parents ab11bdc + 09aadee
commit b78eb1d
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Showing 4 changed files with 40 additions and 44 deletions.
diff --git a/mache/cime_machine_config/config_machines.xml b/mache/cime_machine_config/config_machines.xml
@@ -267,6 +267,7 @@
       <env name="HDF5_USE_FILE_LOCKING">FALSE</env>
       <env name="PERL5LIB">/global/cfs/cdirs/e3sm/perl/lib/perl5-only-switch</env>
       <env name="FI_CXI_RX_MATCH_MODE">software</env>
+      <env name="FI_MR_CACHE_MONITOR">kdreg2</env>
       <env name="MPICH_COLL_SYNC">MPI_Bcast</env>
       <env name="NETCDF_PATH">$ENV{CRAY_NETCDF_HDF5PARALLEL_PREFIX}</env>
       <env name="PNETCDF_PATH">$ENV{CRAY_PARALLEL_NETCDF_PREFIX}</env>
@@ -437,6 +438,7 @@
       <env name="OMP_PLACES">threads</env>
       <env name="HDF5_USE_FILE_LOCKING">FALSE</env>
       <env name="PERL5LIB">/global/cfs/cdirs/e3sm/perl/lib/perl5-only-switch</env>
+      <env name="FI_MR_CACHE_MONITOR">kdreg2</env>
       <env name="MPICH_COLL_SYNC">MPI_Bcast</env>
       <env name="NETCDF_PATH">$ENV{CRAY_NETCDF_HDF5PARALLEL_PREFIX}</env>
       <env name="PNETCDF_PATH">$ENV{CRAY_PARALLEL_NETCDF_PREFIX}</env>
@@ -583,6 +585,7 @@
       <env name="HDF5_USE_FILE_LOCKING">FALSE</env>
       <env name="PERL5LIB">/global/cfs/cdirs/e3sm/perl/lib/perl5-only-switch</env>
       <env name="FI_CXI_RX_MATCH_MODE">software</env>
+      <env name="FI_MR_CACHE_MONITOR">kdreg2</env>
       <env name="MPICH_COLL_SYNC">MPI_Bcast</env>
       <env name="NETCDF_PATH">$ENV{CRAY_NETCDF_HDF5PARALLEL_PREFIX}</env>
       <env name="PNETCDF_PATH">$ENV{CRAY_PARALLEL_NETCDF_PREFIX}</env>
@@ -754,6 +757,7 @@
       <env name="OMP_PLACES">threads</env>
       <env name="HDF5_USE_FILE_LOCKING">FALSE</env>
       <env name="PERL5LIB">/global/cfs/cdirs/e3sm/perl/lib/perl5-only-switch</env>
+      <env name="FI_MR_CACHE_MONITOR">kdreg2</env>
       <env name="MPICH_COLL_SYNC">MPI_Bcast</env>
       <env name="NETCDF_PATH">$ENV{CRAY_NETCDF_HDF5PARALLEL_PREFIX}</env>
       <env name="PNETCDF_PATH">$ENV{CRAY_PARALLEL_NETCDF_PREFIX}</env>
@@ -900,6 +904,7 @@
       <env name="HDF5_USE_FILE_LOCKING">FALSE</env>
       <env name="PERL5LIB">/global/cfs/cdirs/e3sm/perl/lib/perl5-only-switch</env>
       <env name="FI_CXI_RX_MATCH_MODE">software</env>
+      <env name="FI_MR_CACHE_MONITOR">kdreg2</env>
       <env name="MPICH_COLL_SYNC">MPI_Bcast</env>
       <env name="NETCDF_PATH">$ENV{CRAY_NETCDF_HDF5PARALLEL_PREFIX}</env>
       <env name="PNETCDF_PATH">$ENV{CRAY_PARALLEL_NETCDF_PREFIX}</env>
@@ -1067,6 +1072,7 @@
       <cmd_path lang="python">/usr/share/lmod/lmod/libexec/lmod python</cmd_path>
       <modules compiler="crayclang.*">
         <command name="reset"></command>
+        <command name="switch">Core/24.07</command>
         <command name="switch">PrgEnv-cray PrgEnv-cray/8.3.3</command>
         <command name="switch">cce cce/15.0.1</command>
         <!-- craype module to address tcmalloc runtime errors at startup -->
@@ -1079,6 +1085,7 @@
       </modules>
       <modules compiler="amdclang.*">
         <command name="reset"></command>
+        <command name="switch">Core/24.07</command>
         <command name="switch">PrgEnv-cray PrgEnv-amd/8.3.3</command>
         <command name="switch">amd amd/5.4.0</command>
       </modules>
@@ -1087,6 +1094,7 @@
       </modules>
       <modules compiler="gnu.*">
         <command name="reset"></command>
+        <command name="switch">Core/24.07</command>
         <command name="switch">PrgEnv-cray PrgEnv-gnu/8.3.3</command>
         <command name="switch">gcc gcc/12.2.0</command>
       </modules>
@@ -1095,12 +1103,12 @@
         <command name="load">rocm/5.4.0</command>
       </modules>
       <modules>
-        <command name="load">cray-python/3.9.13.1</command>
+        <command name="load">cray-python/3.11.5</command>
         <command name="load">cray-libsci</command>
-        <command name="load">subversion/1.14.1</command>
-        <command name="load">git/2.36.1</command>
-        <command name="load">cmake/3.21.3</command>
-        <command name="load">zlib/1.2.11</command>
+        <command name="load">cmake/3.27.9</command>
+        <command name="load">subversion</command>
+        <command name="load">git</command>
+        <command name="load">zlib</command>
         <command name="load">cray-hdf5-parallel/1.12.2.1</command>
         <command name="load">cray-netcdf-hdf5parallel/4.9.0.1</command>
         <command name="load">cray-parallel-netcdf/1.12.3.1</command>
@@ -2404,17 +2412,15 @@ commented out until "*** No rule to make target '.../libadios2pio-nm-lib.a'" iss
       <modules compiler="intel" mpilib="openmpi">
         <command name="load">openmpi/4.1.6-2mm63n2</command>
         <command name="load">hdf5/1.10.7-4cghwvq</command>
-        <command name="load">netcdf-c/4.4.1-a4hji6e</command>
-        <command name="load">netcdf-cxx/4.2-ldoxr43</command>
-        <command name="load">netcdf-fortran/4.4.4-husened</command>
+        <command name="load">netcdf-c/4.7.4-4qjdadt</command>
+        <command name="load">netcdf-fortran/4.5.3-qozrykr</command>
         <command name="load">parallel-netcdf/1.11.0-icrpxty</command>
       </modules>
       <modules compiler="intel" mpilib="impi">
         <command name="load">intel-mpi/2019.9.304-tkzvizk</command>
-        <command name="load">hdf5/1.8.16-se4xyo7</command>
-        <command name="load">netcdf-c/4.4.1-qvxyzq2</command>
-        <command name="load">netcdf-cxx/4.2-binixgj</command>
-        <command name="load">netcdf-fortran/4.4.4-rdxohvp</command>
+        <command name="load">hdf5/1.10.7-wczt56s</command>
+        <command name="load">netcdf-c/4.7.4-ba6agmb</command>
+        <command name="load">netcdf-fortran/4.5.3-5lvy5p4</command>
         <command name="load">parallel-netcdf/1.11.0-b74wv4m</command>
       </modules>
       <modules compiler="gnu">
@@ -2424,17 +2430,19 @@ commented out until "*** No rule to make target '.../libadios2pio-nm-lib.a'" iss
       <modules compiler="gnu" mpilib="openmpi">
         <command name="load">openmpi/4.1.6-ggebj5o</command>
         <command name="load">hdf5/1.10.7-ol6xuae</command>
-        <command name="load">netcdf-c/4.4.1-2njo6xx</command>
-        <command name="load">netcdf-cxx/4.2-7pdzqua</command>
-        <command name="load">netcdf-fortran/4.4.4-52c6oqi</command>
+        <command name="load">netcdf-c/4.7.4-pfocec2</command>
+        <command name="load">netcdf-fortran/4.5.3-va3hoor</command>
         <command name="load">parallel-netcdf/1.11.0-d7h4ysd</command>
       </modules>
       <modules compiler="gnu" mpilib="impi">
+        <command name="unload">gcc/11.2.0-bgddrif</command>
+        <command name="unload">intel-oneapi-mkl/2022.1.0-w4kgsn4</command>
+        <command name="load">gcc/9.2.0-ugetvbp</command>
+        <command name="load">intel-mkl/2020.4.304-n3b5fye</command>
         <command name="load">intel-mpi/2019.9.304-jdih7h5</command>
         <command name="load">hdf5/1.8.16-dtbpce3</command>
-        <command name="load">netcdf-c/4.4.1-zcoa44z</command>
-        <command name="load">netcdf-cxx/4.2-ayxg4c7</command>
-        <command name="load">netcdf-fortran/4.4.4-2lfr2lr</command>
+        <command name="load">netcdf-c/4.7.4-seagl7g</command>
+        <command name="load">netcdf-fortran/4.5.3-ova6t37</command>
         <command name="load">parallel-netcdf/1.11.0-ifdodru</command>
       </modules>
       <modules compiler="oneapi-ifx">

diff --git a/mache/spack/chrysalis_gnu_openmpi.yaml b/mache/spack/chrysalis_gnu_openmpi.yaml
@@ -109,28 +109,24 @@ spack:
     hdf5:
       externals:
       - spec: [email protected]+cxx+fortran+hl+mpi
-        prefix: /gpfs/fs1/soft/chrysalis/spack/opt/spack/linux-centos8-x86_64/gcc-11.2.0/hdf5-1.10.7-ol6xuae
         modules:
         - hdf5/1.10.7-ol6xuae
       buildable: false
     netcdf-c:
       externals:
-      - spec: [email protected]+mpi~parallel-netcdf
-        prefix: /gpfs/fs1/soft/chrysalis/spack/opt/spack/linux-centos8-x86_64/gcc-11.2.0/netcdf-c-4.4.1-2njo6xx
+      - spec: [email protected]+mpi~parallel-netcdf
         modules:
-        - netcdf-c/4.4.1-2njo6xx
+        - netcdf-c/4.7.4-pfocec2
       buildable: false
     netcdf-fortran:
       externals:
-      - spec: [email protected]
-        prefix: /gpfs/fs1/soft/chrysalis/spack/opt/spack/linux-centos8-x86_64/gcc-11.2.0/netcdf-fortran-4.4.4-52c6oqi
+      - spec: [email protected]
         modules:
-        - netcdf-fortran/4.4.4-52c6oqi
+        - netcdf-fortran/4.5.3-va3hoor
       buildable: false
     parallel-netcdf:
       externals:
       - spec: [email protected]+cxx+fortran
-        prefix: /gpfs/fs1/soft/chrysalis/spack/opt/spack/linux-centos8-x86_64/gcc-11.2.0/parallel-netcdf-1.11.0-d7h4ysd
         modules:
         - parallel-netcdf/1.11.0-d7h4ysd
       buildable: false

diff --git a/mache/spack/chrysalis_intel_impi.yaml b/mache/spack/chrysalis_intel_impi.yaml
@@ -108,29 +108,25 @@ spack:
 {% if e3sm_hdf5_netcdf %}
     hdf5:
       externals:
-      - spec: [email protected]+cxx+fortran+hl+mpi~shared
-        prefix: /gpfs/fs1/soft/chrysalis/spack/opt/spack/linux-centos8-x86_64/intel-20.0.4/hdf5-1.8.16-se4xyo7
+      - spec: [email protected]+cxx+fortran+hl+mpi~shared
         modules:
-        - hdf5/1.8.16-se4xyo7
+        - hdf5/1.10.7-wczt56s
       buildable: false
     netcdf-c:
       externals:
-      - spec: [email protected]+mpi~parallel-netcdf
-        prefix: /gpfs/fs1/soft/chrysalis/spack/opt/spack/linux-centos8-x86_64/intel-20.0.4/netcdf-c-4.4.1-qvxyzq2
+      - spec: [email protected]+mpi~parallel-netcdf
         modules:
-        - netcdf-c/4.4.1-qvxyzq2
+        - netcdf-c/4.7.4-ba6agmb
       buildable: false
     netcdf-fortran:
       externals:
-      - spec: [email protected]
-        prefix: /gpfs/fs1/soft/chrysalis/spack/opt/spack/linux-centos8-x86_64/intel-20.0.4/netcdf-fortran-4.4.4-rdxohvp
+      - spec: [email protected]
         modules:
-        - netcdf-fortran/4.4.4-rdxohvp
+        - netcdf-fortran/4.5.3-5lvy5p4
       buildable: false
     parallel-netcdf:
       externals:
       - spec: [email protected]+cxx+fortran
-        prefix: /gpfs/fs1/soft/chrysalis/spack/opt/spack/linux-centos8-x86_64/intel-20.0.4/parallel-netcdf-1.11.0-b74wv4m
         modules:
         - parallel-netcdf/1.11.0-b74wv4m
       buildable: false

diff --git a/mache/spack/chrysalis_intel_openmpi.yaml b/mache/spack/chrysalis_intel_openmpi.yaml
@@ -109,28 +109,24 @@ spack:
     hdf5:
       externals:
       - spec: [email protected]+cxx+fortran+hl+mpi
-        prefix: /gpfs/fs1/soft/chrysalis/spack/opt/spack/linux-centos8-x86_64/intel-20.0.4/hdf5-1.10.7-4cghwvq
         modules:
         - hdf5/1.10.7-4cghwvq
       buildable: false
     netcdf-c:
       externals:
-      - spec: [email protected]+mpi~parallel-netcdf
-        prefix: /gpfs/fs1/soft/chrysalis/spack/opt/spack/linux-centos8-x86_64/intel-20.0.4/netcdf-c-4.4.1-a4hji6e
+      - spec: [email protected]+mpi~parallel-netcdf
         modules:
-        - netcdf-c/4.4.1-a4hji6e
+        - netcdf-c/4.7.4-4qjdadt
       buildable: false
     netcdf-fortran:
       externals:
-      - spec: [email protected]
-        prefix: /gpfs/fs1/soft/chrysalis/spack/opt/spack/linux-centos8-x86_64/intel-20.0.4/netcdf-fortran-4.4.4-husened
+      - spec: [email protected]
         modules:
-        - netcdf-fortran/4.4.4-husened
+        - netcdf-fortran/4.5.3-qozrykr
       buildable: false
     parallel-netcdf:
       externals:
       - spec: [email protected]+cxx+fortran
-        prefix: /gpfs/fs1/soft/chrysalis/spack/opt/spack/linux-centos8-x86_64/intel-20.0.4/parallel-netcdf-1.11.0-icrpxty
         modules:
         - parallel-netcdf/1.11.0-icrpxty
       buildable: false