buildblocks issueshttps://gitlab.psi.ch/Pmodules/buildblocks/-/issues2024-03-20T16:33:55+01:00https://gitlab.psi.ch/Pmodules/buildblocks/-/issues/274.config-$V_PKG gets wrong Systems output2024-03-20T16:33:55+01:00germann_e.config-$V_PKG gets wrong Systems outputGot
```
cat /opt/psi/Programming/modulefiles/nvhpc/.config-24.3
relstage: unstable
Systems: [merlin-*
ra-]
```
as output, which got me the error:
```
germann_e@merlin-l-001:~/.../Programming/nvhpc$ ./build 24.3 --update-modulefiles...Got
```
cat /opt/psi/Programming/modulefiles/nvhpc/.config-24.3
relstage: unstable
Systems: [merlin-*
ra-]
```
as output, which got me the error:
```
germann_e@merlin-l-001:~/.../Programming/nvhpc$ ./build 24.3 --update-modulefiles
/opt/psi/Tools/Pmodules/1.1.17/bin/modbuild ./build 24.3 --update-modulefiles
Using YAML configuration file - /psi/home/germann_e/buildblocks/Programming/nvhpc/files/config.yaml
nvhpc/24.3: building ...
nvhpc/24.3:
nvhpc/24.3: already exists, not rebuilding ...
nvhpc/24.3: adding modulefile to overlay 'base' ...
/afs/psi.ch/sys/psi.merlin/Tools/Pmodules/1.1.17/bin/../lib/libpbuild.bash: line 1520: local: `ra-': invalid variable name for name reference
* * * * *
```https://gitlab.psi.ch/Pmodules/buildblocks/-/issues/273config.yaml doesn't take into account --with nvhpc/24.32024-03-20T16:34:52+01:00germann_econfig.yaml doesn't take into account --with nvhpc/24.3With the following config.yaml
# config.yaml
```
4.1.5:
variants:
- systems: [merlin-*, ra-*]
suffix: _slurm
group_deps:
compiler: {gcc: [9.5.0, 10.4.0, 11.4.0, 12.3.0, 13.1.0]}
...With the following config.yaml
# config.yaml
```
4.1.5:
variants:
- systems: [merlin-*, ra-*]
suffix: _slurm
group_deps:
compiler: {gcc: [9.5.0, 10.4.0, 11.4.0, 12.3.0, 13.1.0]}
build_requires: [pmix/4.2.4, ucx/1.14.1_slurm, libfabric/1.18.0, hwloc/2.9.1, patchelf/0.14.5]
runtime_deps: [cuda/12.1.1]
- systems: [merlin-*, ra-*]
suffix: _slurm
relstage: unstable
group_deps:
compiler: {intelcc: [22.2]}
build_requires: [pmix/4.2.4, ucx/1.14.1_slurm, libfabric/1.18.0, hwloc/2.9.1, patchelf/0.14.5]
runtime_deps: [cuda/12.1.1]
- systems: [merlin-*, ra-*]
suffix: _slurm
relstage: unstable
group_deps:
compiler: {nvhpc: [24.3]}
build_requires: [pmix/4.2.4, ucx/1.14.1_slurm, libfabric/1.18.0, hwloc/2.9.1, patchelf/0.14.5]
```
& the command
```
germann_e@merlin-l-001:~/.../Compiler/openmpi$ ./build 4.1.5 --with nvhpc/24.3 --update-modulefiles
/opt/psi/Tools/Pmodules/1.1.17/bin/modbuild ./build 4.1.5 --with nvhpc/24.3 --update-modulefiles
Using YAML configuration file - /psi/home/germann_e/buildblocks/Compiler/openmpi/files/config.yaml
openmpi/4.1.5_slurm: with gcc/9.5.0 cuda/12.1.1 b:pmix/4.2.4 b:ucx/1.14.1_slurm b:libfabric/1.18.0 b:hwloc/2.9.1 b:patchelf/0.14.5 building ...
Loading module: gcc/9.5.0
Loading module: cuda/12.1.1
Loading module: pmix/4.2.4
Loading module: ucx/1.14.1_slurm
Loading module: libfabric/1.18.0
Loading module: hwloc/2.9.1
Loading module: patchelf/0.14.5
Using pbuild::set_download_url is deprecated with YAML module configuration files.
Using pbuild::set_sha256sum is deprecated with YAML module configuration files.
Using pbuild::add_to_group is deprecated with YAML module configuration files.
Using pbuild::install_docfiles is deprecated with YAML module configuration files.
openmpi/4.1.5_slurm: build with gcc/9.5.0 cuda/12.1.1 b:pmix/4.2.4 b:ucx/1.14.1_slurm b:libfabric/1.18.0 b:hwloc/2.9.1 b:patchelf/0.14.5
openmpi/4.1.5_slurm: already exists, not rebuilding ...
openmpi/4.1.5_slurm: adding modulefile to overlay 'base' ...
* * * * *
openmpi/4.1.5_slurm: with gcc/10.4.0 cuda/12.1.1 b:pmix/4.2.4 b:ucx/1.14.1_slurm b:libfabric/1.18.0 b:hwloc/2.9.1 b:patchelf/0.14.5 building ...
Loading module: gcc/10.4.0
Loading module: cuda/12.1.1
Loading module: pmix/4.2.4
```
The build binary is still trying to compile with all the compilers (gcc, intelcc) though --with nvhpc is given.https://gitlab.psi.ch/Pmodules/buildblocks/-/issues/272test2024-03-19T17:39:41+01:00gselltestgsellgsellhttps://gitlab.psi.ch/Pmodules/buildblocks/-/issues/271build new pmodule finddqe2023-12-05T08:40:26+01:00assman_gbuild new pmodule finddqehttps://gitlab.psi.ch/Pmodules/buildblocks/-/issues/270tmux/3.2 change rel-stage to stable2023-08-04T13:49:53+02:00gselltmux/3.2 change rel-stage to stablegsellgsellhttps://gitlab.psi.ch/Pmodules/buildblocks/-/issues/269new module for redis2023-08-04T11:37:41+02:00gsellnew module for redisgsellgsellhttps://gitlab.psi.ch/Pmodules/buildblocks/-/issues/268gtest: download url has hardcoded version2023-07-17T13:20:12+02:00gsellgtest: download url has hardcoded versiongsellgsellhttps://gitlab.psi.ch/Pmodules/buildblocks/-/issues/267toolchain for IPPL/OPAL with gcc/12.3.02024-03-19T17:42:40+01:00gselltoolchain for IPPL/OPAL with gcc/12.3.0gsellgsellhttps://gitlab.psi.ch/Pmodules/buildblocks/-/issues/266fftw 3.3.10 for merlin with gcc/10.4.0 and openmpi/4.1.5_merlin62023-07-10T15:55:48+02:00gsellfftw 3.3.10 for merlin with gcc/10.4.0 and openmpi/4.1.5_merlin6gsellgsellhttps://gitlab.psi.ch/Pmodules/buildblocks/-/issues/265build modules for current mpfr and mpc2023-07-13T15:59:36+02:00gsellbuild modules for current mpfr and mpcgsellgsellhttps://gitlab.psi.ch/Pmodules/buildblocks/-/issues/264build modules for current gcc's2023-07-13T15:56:01+02:00gsellbuild modules for current gcc'sgsellgsellhttps://gitlab.psi.ch/Pmodules/buildblocks/-/issues/263GPU support in EMAN2023-05-12T09:26:14+02:00bliven_sGPU support in EMANEMAN/2.99.47 does not appear to have GPU support. Tensorflow uses the cpu package:
```
$ module load EMAN/2.99.47 cuda/11.2.2
$ conda list tensorflow
# packages in environment at /opt/psi/EM/EMAN/2.99.47:
#
# Name Ve...EMAN/2.99.47 does not appear to have GPU support. Tensorflow uses the cpu package:
```
$ module load EMAN/2.99.47 cuda/11.2.2
$ conda list tensorflow
# packages in environment at /opt/psi/EM/EMAN/2.99.47:
#
# Name Version Build Channel
tensorflow 2.11.0 cpu_py39h4655687_0 conda-forge
tensorflow-base 2.11.0 cpu_py39h9b4020c_0 conda-forge
tensorflow-estimator 2.11.0 cpu_py39hf050123_0 conda-forge
$ python -c 'import tensorflow as tf; print(tf.compat.v1.Session(config=tf.compat.v1.ConfigProto(log_device_placement=True)))'
2023-05-10 16:47:39.596002: I tensorflow/core/platform/cpu_feature_guard.cc:193] This TensorFlow binary is optimized with oneAPI Deep Neural Network Library (oneDNN) to use the following CPU instructions in performance-critical operations: SSE4.1 SSE4.2 AVX AVX2 FMA
To enable them in other operations, rebuild TensorFlow with the appropriate compiler flags.
2023-05-10 16:48:40.478528: I tensorflow/core/platform/cpu_feature_guard.cc:193] This TensorFlow binary is optimized with oneAPI Deep Neural Network Library (oneDNN) to use the following CPU instructions in performance-critical operations: SSE4.1 SSE4.2 AVX AVX2 FMA
To enable them in other operations, rebuild TensorFlow with the appropriate compiler flags.
2023-05-10 16:48:40.482778: I tensorflow/core/common_runtime/direct_session.cc:370] Device mapping: no known devices.
<tensorflow.python.client.session.Session object at 0x7f7454f10340>
```
According to [this](https://blake.bcm.edu/emanwiki/EMAN2/Install/BinaryInstallAnaconda/2.99#GPU) it is probably possible to just reinstall tensorflow after loading the cuda toolkit. Cuda should be a dependency of the pmodule as well.
germann_egermann_ehttps://gitlab.psi.ch/Pmodules/buildblocks/-/issues/262new build-block GNU parallel2023-07-13T16:23:12+02:00gsellnew build-block GNU parallelgsellgsellhttps://gitlab.psi.ch/Pmodules/buildblocks/-/issues/261vim 8.12023-07-13T16:26:28+02:00gsellvim 8.1gsellgsellhttps://gitlab.psi.ch/Pmodules/buildblocks/-/issues/260new build-block for moreutils2023-07-13T16:34:26+02:00gsellnew build-block for moreutilsgsellgsellhttps://gitlab.psi.ch/Pmodules/buildblocks/-/issues/259new build-block for gdb2023-07-13T16:19:50+02:00gsellnew build-block for gdbgsellgsellhttps://gitlab.psi.ch/Pmodules/buildblocks/-/issues/258add aws cli as a new pmodule2024-02-27T11:31:57+01:00pozsa_kadd aws cli as a new pmodulepozsa_kpozsa_khttps://gitlab.psi.ch/Pmodules/buildblocks/-/issues/257build cmake/3.25.22023-07-13T16:04:20+02:00gsellbuild cmake/3.25.2gsellgsellhttps://gitlab.psi.ch/Pmodules/buildblocks/-/issues/256HDF5_blosc: deprecate version compiled with a deprecated compiler2023-01-27T15:38:24+01:00gsellHDF5_blosc: deprecate version compiled with a deprecated compilergsellgsellhttps://gitlab.psi.ch/Pmodules/buildblocks/-/issues/255git-lfs module2023-01-27T15:45:41+01:00gsellgit-lfs modulegsellgsell