Update environment with file from cobalt

README.md

@@ -20,6 +20,7 @@ The next step is to install the dependencies of the COBALT software through Spac
 ```bash
 spack env create lofar
 spack env activate lofar
+source ${SPACK_DIR}/share/spack/setup-env.sh
 cp environment.yaml $SPACK_ENV/spack.yaml
 spack install
 ```
@@ -46,9 +47,9 @@ module use /opt/spack/0.22.1/share/spack/modules/linux-debian12-zen2/gcc/12.2.0
 ## Building COBALT from source
 Now that all the prerequisites are met, the COBALT software can be installed as follows:
 ```bash
-git clone https://git.astron.nl/lofar2.0/cobalt
+git clone https://git.astron.nl/lofar2.0/cobalt.git
 cd cobalt
-source configure.sh
+source ../configure.sh
 make -C gnucxx11_opt/ -j
 ```
 

environment.yaml

 spack:
   specs:
-  - cuda@12.4
-  - dal2
+  - curl
   - pqxx@6.4.8
+  - dal2@master
   - binutils@2.30
   - boost+date_time+regex+filesystem+system+python+numpy
-  #- hdf5 +cxx+hl+threadsafe~mpi
+  - hdf5@1.14.4-3 +cxx+hl+threadsafe~mpi
   - openblas threads=pthreads
   - fftw
-  - casacore
+  - casacore@3.5.0
   - log4cplus
-  #- qpid
-  #- py-kombu
-  #- py-casacore
-  #- py-lxml
+  - py-kombu
+  - py-lxml
   - readline
-  - curl
   - ncurses
   - postgresql
-  - openmpi fabrics=verbs
+  - openmpi fabrics=verbs,ucx ^ucx+dc+rc+verbs+rdmacm
+  - numactl
+  - python
   - numactl
-  #- python
-#  - numactl
+  - cmake@3.28.6
   - autogen
-  - unittest-cpp
+  - unittest-cpp@1.6.0
   - curl
+  - gdb
+  - python@3.11.9
+  - osu-micro-benchmarks
   view: false
   concretizer:
     unify: true
+  repos:
+    - /opt/spack/repos/ska-sdp-spack
   compilers:
     - compiler:
         spec: gcc@=12.2.0
@@ -42,3 +45,15 @@ spack:
         modules: []
         environment: {}
         extra_rpaths: []
+  modules:
+    default:
+      enable:
+        - tcl
+      tcl:
+        hash_length: 0
+        naming_scheme: '{compiler.name}/{compiler.version}/{name}/{version}'
+        all:
+          environment:
+            set:
+              '{name}_ROOT': '{prefix}'
+          autoload: none
\ No newline at end of file

infra/install_cobalt.sh

@@ -38,7 +38,7 @@ echo -e "repos:\n- ${SPACK_REPO_DIR}/ska-sdp-spack" > $HOME/.spack/repos.yaml
 ${SPACK_DIR}/bin/spack env create lofar
 
 # use spack environment
-#source ${SPACK_DIR}/share/spack/setup-env.sh
+source ${SPACK_DIR}/share/spack/setup-env.sh
 eval `${SPACK_DIR}/bin/spack env activate --sh lofar`
 
 # make sure no modules are messing with the environment,

old-environment.yaml

+spack:
+  specs:
+  - cuda@12.4
+  - dal2
+  - pqxx@6.4.8
+  - binutils@2.30
+  - boost+date_time+regex+filesystem+system+python+numpy
+  #- hdf5 +cxx+hl+threadsafe~mpi
+  - openblas threads=pthreads
+  - fftw
+  - casacore
+  - log4cplus
+  #- qpid
+  #- py-kombu
+  #- py-casacore
+  #- py-lxml
+  - readline
+  - curl
+  - ncurses
+  - postgresql
+  - openmpi fabrics=verbs
+  - numactl
+  #- python
+#  - numactl
+  - autogen
+  - unittest-cpp
+  view: false
+  concretizer:
+    unify: true
+  compilers:
+  - compiler:
+      spec: gcc@=12.2.0
+      paths:
+        cc: /usr/bin/gcc
+        cxx: /usr/bin/g++
+        f77: /usr/bin/gfortran
+        fc: /usr/bin/gfortran
+      flags: {}
+      operating_system: debian12
+      target: x86_64
+      modules: []
+      environment: {}
+      extra_rpaths: []