software.hpc: Tracking PR

.gitignore

@@ -11,3 +11,4 @@ __pycache__
 **/#*#
 
 files/
+.cvmfscatalog

bin/wrappers/deepemhancer-cryosparc

@@ -0,0 +1,18 @@
+#!/bin/bash -l
+if command -v conda > /dev/null 2>&1; then
+    conda deactivate > /dev/null 2>&1 || true  # ignore any errors
+    conda deactivate > /dev/null 2>&1 || true  # ignore any errors
+fi
+unset _CE_CONDA
+unset CONDA_DEFAULT_ENV
+unset CONDA_EXE
+unset CONDA_PREFIX
+unset CONDA_PROMPT_MODIFIER
+unset CONDA_PYTHON_EXE
+unset CONDA_SHLVL
+unset PYTHONPATH
+unset LD_PRELOAD
+unset LD_LIBRARY_PATH
+
+module load conda/deepemhancer
+exec deepemhancer --deepLearningModelPath /share/databases/deepemhancer/models $@

bin/wrappers/topaz

@@ -0,0 +1,3 @@
+#!/bin/bash -l
+module load conda/topaz
+topaz $@

bin/wrappers/topaz-cryosparc

@@ -0,0 +1,18 @@
+#!/bin/bash -l
+if command -v conda > /dev/null 2>&1; then
+    conda deactivate > /dev/null 2>&1 || true  # ignore any errors
+    conda deactivate > /dev/null 2>&1 || true  # ignore any errors
+fi
+unset _CE_CONDA
+unset CONDA_DEFAULT_ENV
+unset CONDA_EXE
+unset CONDA_PREFIX
+unset CONDA_PROMPT_MODIFIER
+unset CONDA_PYTHON_EXE
+unset CONDA_SHLVL
+unset PYTHONPATH
+unset LD_PRELOAD
+unset LD_LIBRARY_PATH
+
+module load conda/topaz
+exec topaz $@

config/hpccf/farm/v0.19.1/packages.yaml

@@ -1,98 +1,52 @@
 packages:
-  #gettext:
-  #  externals:
-  #  - spec: [email protected]
-  #    prefix: /usr
-  #  buildable: false
-  pkg-config:
-    externals:
-    - spec: [email protected]
-      prefix: /usr
-    buildable: false
-  curl:
-    externals:
-    - spec: [email protected]+gssapi+ldap+nghttp2
-      prefix: /usr
-  bash:
-    externals:
-    - spec: [email protected]
-      prefix: /usr
-    buildable: false
-  munge:
-    externals:
-    - spec: [email protected] %[email protected]
-      prefix: /usr
-    buildable: false
-  mariadb:
-    externals:
-    - spec: [email protected] %[email protected]
-      prefix: /usr
-    buildable: false
-  mariadb-c-client:
-    externals:
-    - spec: mariadb-c-client@3 %[email protected]
-      prefix: /usr
+  ####
+  # Externals: non-buildable
+  ####
+
   at-spi2-core:
     externals:
     - spec: [email protected] %[email protected]
       prefix: /usr
     buildable: false
+
   at-spi2-atk:
     externals:
     - spec: [email protected] %[email protected]
       prefix: /usr
     buildable: false
+
   atk:
     externals:
     - spec: [email protected]
       prefix: /usr
     buildable: false
-  gtkplus:
-    buildable: false
-    externals:
-    - spec: [email protected]
-      prefix: /usr
-    - spec: [email protected]
-      prefix: /usr
-  opengl:
-    buildable: false
+
+  bash:
     externals:
-    - spec: [email protected] %[email protected]
+    - spec: [email protected]
       prefix: /usr
-  linux-pam:
     buildable: false
-    externals:
-    - spec: [email protected] %[email protected]
-      prefix: /usr
-  openssl:
-    externals:
-    - spec: [email protected]
-      prefix: /usr
-    #buildable: False
 
-  rust:
-    externals:
-    - spec: [email protected]
-      prefix: /usr
   cvs:
     buildable: false
     externals:
     - spec: [email protected]
       prefix: /usr
-  subversion:
+
+  gtkplus:
     buildable: false
     externals:
-    - spec: [email protected]
+    - spec: [email protected]
       prefix: /usr
-  llvm:
+    - spec: [email protected]
+      prefix: /usr
+
+  pkg-config:
     externals:
-    - spec: [email protected]+clang~lld~lldb
+    - spec: [email protected]
       prefix: /usr
-      extra_attributes:
-        compilers:
-          c: /usr/bin/clang-14
-          cxx: /usr/bin/clang++-14
-
+    buildable: false
+
   julia:
     buildable: false
     externals:
@@ -110,69 +64,169 @@ packages:
     externals:
     - spec: [email protected] +pmix +mariadb +hwloc +restd
       prefix: /share/apps/22.04/slurm/22.05.9.p2
+
   hwloc:
     buildable: false
     externals:
     - spec: [email protected]
       prefix: /share/apps/22.04/hwloc/2.9.3
+
   pmix:
     buildable: false
     externals:
     - spec: [email protected]
       prefix: /share/apps/22.04/pmix/4.2.6
+
   ucx:
     buildable: false
     externals:
     - spec: [email protected] +thread_multiple
       prefix: /share/apps/22.04/ucx/1.14.1
+
   libevent:
     buildable: false
     externals:
     - spec: [email protected]
       prefix: /share/apps/22.04/libevent/2.1.12-stable
+
+  linux-pam:
+    buildable: false
+    externals:
+    - spec: [email protected] %[email protected]
+      prefix: /usr
+
+  mariadb:
+    externals:
+    - spec: [email protected] %[email protected]
+      prefix: /usr
+    buildable: false
+
+  mariadb-c-client:
+    externals:
+    - spec: mariadb-c-client@3 %[email protected]
+      prefix: /usr
+
+  munge:
+    externals:
+    - spec: [email protected] %[email protected]
+      prefix: /usr
+    buildable: false
+
+  opengl:
+    buildable: false
+    externals:
+    - spec: [email protected] %[email protected]
+      prefix: /usr
+
   openmpi:
     buildable: false
     externals:
     - spec: [email protected] fabrics=ucx schedulers=slurm +cuda
       prefix: /share/apps/22.04/openmpi/4.1.5
-  ##########
 
-  intel-mkl:
-    require: '@2017.0.098:'
-  mpi:
-    require: openmpi
-  tbb:
-    require: intel-oneapi-tbb
-  mkl:
-    require: intel-oneapi-mkl
-  dbus:
-    require: '@1.12.8 local_state_dir=/var/'
-  cairo:
-    require: +X +ft +fc +pdf +png +gobject
-  python:
-    require: ~libxml2
-  libxml2:
-    require: '@2.10.2: +python'
-  lmod:
-    require: '@8.7.14 modulepath_root=/share/apps/spack/modulefiles/'
-    version:
-    - 8.7.14
-    variants: modulepath_root=/share/apps/spack/modulefiles/
+
+
+  subversion:
+    buildable: false
+    externals:
+    - spec: [email protected]
+      prefix: /usr
+
+
+  ####
+  # Externals: buildable
+  ####
+  #
+
+  curl:
+    externals:
+    - spec: [email protected]+gssapi+ldap+nghttp2
+      prefix: /usr
+
+  llvm:
+    externals:
+    - spec: [email protected]+clang~lld~lldb
+      prefix: /usr
+      extra_attributes:
+        compilers:
+          c: /usr/bin/clang-14
+          cxx: /usr/bin/clang++-14
+
+  openssl:
+    externals:
+    - spec: [email protected]
+      prefix: /usr
+
+  rust:
+    externals:
+    - spec: [email protected]
+      prefix: /usr
+
+  ####
+  # Package requirements and variants
+  ####
+  #
+
   amdfftw:
     require: '@3.2 +openmp'
     version:
     - 3.2
     variants: +openmp
-  intel-oneapi-mkl:
-    require: '@2022.2.1'
-    version:
-    - 2022.2.1
+
+  cairo:
+    require: +X +ft +fc +pdf +png +gobject
+
+  dbus:
+    require: '@1.12.8 local_state_dir=/var/'
 
   fftw:
     require: '@3.3.10 +openmp'
     version:
     - 3.3.10
     variants: +openmp
+
+  gdal:
+    variants: +netcdf +sqlite3 +xml2 +grib +hdf5 +curl +geos +cfitsio +crypto +expat
+      +gif +jasper +pcre +png +zstd
+  gdl:
+    version: [0.9.9]
+    variants: +graphicsmagick +python
+
+  hdf5:
+    variants: +fortran +hl
+
+  intel-mkl:
+    require: '@2017.0.098:'
+
+  intel-oneapi-mkl:
+    require: '@2022.2.1'
+    version:
+    - 2022.2.1
+
+  libxml2:
+    require: '@2.10.2: +python'
+
+  lmod:
+    require: '@8.7.14 modulepath_root=/share/apps/spack/modulefiles/'
+    version:
+    - 8.7.14
+    variants: modulepath_root=/share/apps/spack/modulefiles/
+
+  mkl:
+    require: intel-oneapi-mkl
+
+  mpi:
+    require: openmpi
+
+  python:
+    require: ~libxml2
+
+  sqlite:
+    variants: +rtree
+
+  tbb:
+    require: intel-oneapi-tbb
+
   ####
 
   all:
@@ -185,14 +239,3 @@ packages:
     variants:
     - cuda_arch=75
 
-  gdal:
-    variants: +netcdf +sqlite3 +xml2 +grib +hdf5 +curl +geos +cfitsio +crypto +expat
-      +gif +jasper +pcre +png +zstd
-  gdl:
-    version: [0.9.9]
-    variants: +graphicsmagick +python
-  sqlite:
-    variants: +rtree
-
-  hdf5:
-    variants: +fortran +hl