esm-environment issueshttps://gitlab.dkrz.de/esm-tools-old-stuff/esm-environment/-/issues2019-09-30T08:55:54Zhttps://gitlab.dkrz.de/esm-tools-old-stuff/esm-environment/-/issues/16Load python module2019-09-30T08:55:54ZNadine WietersLoad python moduleNadine WietersNadine Wietershttps://gitlab.dkrz.de/esm-tools-old-stuff/esm-environment/-/issues/15Update Juwels env2019-09-30T08:56:11ZNadine WietersUpdate Juwels envNadine WietersNadine Wietershttps://gitlab.dkrz.de/esm-tools-old-stuff/esm-environment/-/issues/13Use ParastationMPI on juwels2019-03-04T12:57:30ZNadine WietersUse ParastationMPI on juwelsUsing intelMPI leads to hanging simulations during reading large meshes (e.g. fArc).
A solution is for now, to exchange intelMPI with ParastationMPI in the juwels environment file.Using intelMPI leads to hanging simulations during reading large meshes (e.g. fArc).
A solution is for now, to exchange intelMPI with ParastationMPI in the juwels environment file.Release 2.0Nadine WietersNadine Wietershttps://gitlab.dkrz.de/esm-tools-old-stuff/esm-environment/-/issues/12Buggy behaviour of cdo when loaded via netcdf-tools on ollie2019-02-26T09:30:32ZNadine WietersBuggy behaviour of cdo when loaded via netcdf-tools on ollieNadine WietersNadine Wietershttps://gitlab.dkrz.de/esm-tools-old-stuff/esm-environment/-/issues/11Loading default modules for intel and intelMPI on Juwels2019-01-29T09:21:37ZNadine WietersLoading default modules for intel and intelMPI on JuwelsNadine WietersNadine Wietershttps://gitlab.dkrz.de/esm-tools-old-stuff/esm-environment/-/issues/10Missing/not loaded doxygen module2019-01-23T10:23:30ZNadine WietersMissing/not loaded doxygen moduleModule doxygen is not loaded on juwels.
This module is needed, because doxygen will be called before pushing to repository.Module doxygen is not loaded on juwels.
This module is needed, because doxygen will be called before pushing to repository.Release 2.0Nadine WietersNadine Wietershttps://gitlab.dkrz.de/esm-tools-old-stuff/esm-environment/-/issues/9Runtime error: `CXXABI_1.3.8' not found2019-01-31T09:58:36ZNadine WietersRuntime error: `CXXABI_1.3.8' not foundSee issue
esm-tools/esm-runscripts#137See issue
esm-tools/esm-runscripts#137https://gitlab.dkrz.de/esm-tools-old-stuff/esm-environment/-/issues/8Compiling error on juwels2018-12-20T08:57:54ZNadine WietersCompiling error on juwelsNadine WietersNadine Wietershttps://gitlab.dkrz.de/esm-tools-old-stuff/esm-environment/-/issues/7Load module centoslibs/7.5 on Ollie2018-12-07T13:02:40ZNadine WietersLoad module centoslibs/7.5 on OllieNadine WietersNadine Wietershttps://gitlab.dkrz.de/esm-tools-old-stuff/esm-environment/-/issues/6Update to new netcdf module 4.6.1 on Ollie2019-03-07T15:06:24ZNadine WietersUpdate to new netcdf module 4.6.1 on OllieNadine WietersNadine Wietershttps://gitlab.dkrz.de/esm-tools-old-stuff/esm-environment/-/issues/5compile failed on Juelich2018-10-11T13:24:48ZShizhu Wangcompile failed on JuelichThe compilation of awicm-CMIP6 failed on Juelich, with the error message enclosed.
[error.message](/uploads/f48a44cbc9938cee044eeec9d22d3097/error.message)
@a270077 The code is in `/gpfs/homea/hhb20/hhb203/esm-master`The compilation of awicm-CMIP6 failed on Juelich, with the error message enclosed.
[error.message](/uploads/f48a44cbc9938cee044eeec9d22d3097/error.message)
@a270077 The code is in `/gpfs/homea/hhb20/hhb203/esm-master`https://gitlab.dkrz.de/esm-tools-old-stuff/esm-environment/-/issues/4mistral: missing shared libraries for cdo2018-09-24T13:31:46ZChristopher Danekmistral: missing shared libraries for cdoHi
When I use `awicm-CMIP6` (`release`) on `mistral` with the `esm-environment` version `2626085`, the following error occurs in the `log/awicm/expname_date_expid_esmlog.dump`:
```
Currently Loaded Modulefiles:
1) gcc/4.8.2 ...Hi
When I use `awicm-CMIP6` (`release`) on `mistral` with the `esm-environment` version `2626085`, the following error occurs in the `log/awicm/expname_date_expid_esmlog.dump`:
```
Currently Loaded Modulefiles:
1) gcc/4.8.2 5) nco/4.7.5-gcc64
2) jdk/1.8.0_20 6) intelmpi/2017.0.098
3) intel/18.0.0 7) netcdf_c/4.3.2-gcc48
4) cdo/1.9.5-magicsxx-gcc64 8) cmake/3.5.2
...
cdo: /sw/rhel6-x64/gcc/gcc-4.8.2/lib64/libstdc++.so.6: version `CXXABI_1.3.8' not found (required by cdo)
cdo: /sw/rhel6-x64/gcc/gcc-4.8.2/lib64/libstdc++.so.6: version `GLIBCXX_3.4.21' not found (required by cdo)
cdo: /sw/rhel6-x64/gcc/gcc-4.8.2/lib64/libstdc++.so.6: version `CXXABI_1.3.9' not found (required by cdo)
cdo: /sw/rhel6-x64/gcc/gcc-4.8.2/lib64/libstdc++.so.6: version `GLIBCXX_3.4.20' not found (required by cdo)
cdo: /sw/rhel6-x64/gcc/gcc-4.8.2/lib64/libgomp.so.1: version `GOMP_4.0' not found (required by cdo)
cdo: /sw/rhel6-x64/gcc/gcc-4.8.2/lib64/libgomp.so.1: version `OMP_4.0' not found (required by cdo)
```
Apparently, some shared library dependencies are missing for the new cdo version `1.9.5` and it cannot be executed. For example,
```
ldd /sw/rhel6-x64/cdo/cdo-1.9.5-magicsxx-gcc64/bin/cdo | grep gcc-
libstdc++.so.6 => /sw/rhel6-x64/gcc/gcc-6.4.0/lib64/libstdc++.so.6 (0x00007f41abfa6000)
libgomp.so.1 => /sw/rhel6-x64/gcc/gcc-6.4.0/lib64/libgomp.so.1 (0x00007f41abd79000)
libgcc_s.so.1 => /sw/rhel6-x64/gcc/gcc-6.4.0/lib64/libgcc_s.so.1 (0x00007f4190a2f000)
libgfortran.so.3 => /sw/rhel6-x64/gcc/gcc-4.8.2/lib64/libgfortran.so.3 (0x00007f418eca4000)
libquadmath.so.0 => /sw/rhel6-x64/gcc/gcc-4.8.2/lib64/libquadmath.so.0 (0x00007f418ea69000)
```
shows, that different gcc versions were used for libraries cdo depends on (here gcc 6.4.0 and 4.8.2). So in this case, adding gcc version `6.4.0` to `LD_LIBRARY_PATH` somewhere in the `esm-environment/mistral.dkrz.de` solves the problem.
For doing this in a general way, i.e. not writing specific version numbers into `esm-environment/mistral.dkrz.de`, the following lines may work instead:
```
echo "======== workaround ========"
echo " esm-environment/mistral.dkrz.de:"
echo " Load eventually missing shared library dependencies for cdo with LD_LIBRARY_PATH ..."
echo " execute 'strings -a `which cdo` | grep 'GCC: (' ..."
strings -a `which cdo` | grep 'GCC: (' | while read -r strings_output ; do
echo " $strings_output"
version=`echo $strings_output | awk -F ' ' '{print $3}'`
echo " add /sw/rhel6-x64/gcc/gcc-$version/lib64 to LD_LIBRARY_PATH ..."
export LD_LIBRARY_PATH=/sw/rhel6-x64/gcc/gcc-$version/lib64:$LD_LIBRARY_PATH
done
echo "LD_LIBRARY_PATH: $LD_LIBRARY_PATH"
echo "============================"
```
yields
```
======== workaround ========
esm-environment/mistral.dkrz.de:
Load eventually missing shared library dependencies for cdo with LD_LIBRARY_PATH ...
LD_LIBRARY_PATH: /sw/rhel6-x64/intel/intel-18.0.0/mkl/lib/intel64:/sw/rhel6-x64/intel/intel-18.0.0/lib/intel64:/sw/rhel6-x64/gcc/gcc-4.8.2/lib64:
execute 'strings -a /sw/rhel6-x64/cdo/cdo-1.9.5-magicsxx-gcc64/bin/cdo | grep 'GCC: (' ...
GCC: (GNU) 4.4.7 20120313 (Red Hat 4.4.7-18)
add /sw/rhel6-x64/gcc/gcc-4.4.7/lib64 to LD_LIBRARY_PATH ...
GCC: (GNU) 6.4.0
add /sw/rhel6-x64/gcc/gcc-6.4.0/lib64 to LD_LIBRARY_PATH ...
LD_LIBRARY_PATH: /sw/rhel6-x64/gcc/gcc-6.4.0/lib64:/sw/rhel6-x64/gcc/gcc-4.4.7/lib64:/sw/rhel6-x64/intel/intel-18.0.0/mkl/lib/intel64:/sw/rhel6-x6
4/intel/intel-18.0.0/lib/intel64:/sw/rhel6-x64/gcc/gcc-4.8.2/lib64:
============================
```
in the `log/awicm/expname_expdate_jobid_esmlog.dump` and the errors disappear.
I dont know if this is a nice solution from a programers perspective - certainly not.
Note that using `ldd` would maybe the first choice for checking missing shared library dependencies, however, `ldd` executes the program to be checked (cdo in this case) by itself, which is not possible because of the same error as above.
Chrishttps://gitlab.dkrz.de/esm-tools-old-stuff/esm-environment/-/issues/3super_merge: Merge for release 12018-08-27T12:24:20ZNadine Wieterssuper_merge: Merge for release 1Nadine WietersNadine Wietershttps://gitlab.dkrz.de/esm-tools-old-stuff/esm-environment/-/issues/2Environment for Jülich HPC2018-08-17T11:13:39ZNadine WietersEnvironment for Jülich HPCRelease 1.0Nadine WietersNadine Wietershttps://gitlab.dkrz.de/esm-tools-old-stuff/esm-environment/-/issues/1awicm and mpiesm don't compile on Ollie2018-06-27T12:47:11ZPaul Gierzawicm and mpiesm don't compile on OllieThe new esm-environment tool doesn't work on Ollie yet.The new esm-environment tool doesn't work on Ollie yet.