seissol / pspamm

SeisSol is a scientific software for the numerical simulation of seismic wave phenomena and earthquake dynamics. It is based on the discontinuous Galerkin method combined with ADER time discretization. Visit our official website and also read our documentation in order to learn more about SeisSol. Our discussion forum can help you to communicate with SeisSol developers or other users, share your ideas, ask questions, etc.

Note

SeisSol is still under heavy development and comes without any guaranteed funcitonality. At the moment we can only provide very limited support for general users.

Collaboration

If you are interested in a close collaboration, please, contact Alice Gabriel.

Code of Conduct

We follow a Code of Conduct. Please follow the rules when participating in our community.

Contributing

We will be happy if you plan to contribute new features, extensions or bug fixes to SeisSol. To start off, please, open a new issue and discuss your feature with us before diving into coding. Visit our doxygen documentation to learn more about the source code structure.

To learn more about contributing to SeisSol, please read our Contribution page.

pspamm's Issues

cannot import name 'full' from 'scipy' (scipy 1.12.0, full has been removed with this version)

Installing seissol with (on heisenbug):

CXX=g++ CC=gcc cmake -DNUMA_AWARE_PINNING=ON -DASAGI=ON -DCMAKE_BUILD_TYPE=Release -DHOST_ARCH=hsw -DPRECISION=double -DORDER=4 -DGEMM_TOOLS_LIST=LIBXSMM,PSpaMM .. 

Error log

projectDerivativeToNodalBoundaryRotated (16 AST(s))
subTriangleDisplacement (4 AST(s))
subTriangleVelocity (4 AST(s))
addVelocity (4 AST(s))
Generating kernels...
Calling external code generators...
Traceback (most recent call last):
  File "/import/tegern-data/ulrich/MyLibs/mambaforge3/bin/pspamm-generator", line 5, in <module>
    from pspamm.pspamm import main
  File "/import/exception-dump/ulrich/myLibs/spack-packages/linux-debian11-zen2/gcc-12.2.0/py-pspamm-develop-zwccp4lcotug5pl244tnmo3ftfzzxmix/pspamm/pspamm.py", line 7, in <module>
    from pspamm.matmul import *
  File "/import/exception-dump/ulrich/myLibs/spack-packages/linux-debian11-zen2/gcc-12.2.0/py-pspamm-develop-zwccp4lcotug5pl244tnmo3ftfzzxmix/pspamm/matmul.py", line 13, in <module>
    from pspamm.cursors import *
  File "/import/exception-dump/ulrich/myLibs/spack-packages/linux-debian11-zen2/gcc-12.2.0/py-pspamm-develop-zwccp4lcotug5pl244tnmo3ftfzzxmix/pspamm/cursors/__init__.py", line 1, in <module>
    from pspamm.cursors.matrix import Matrix
  File "/import/exception-dump/ulrich/myLibs/spack-packages/linux-debian11-zen2/gcc-12.2.0/py-pspamm-develop-zwccp4lcotug5pl244tnmo3ftfzzxmix/pspamm/cursors/matrix.py", line 8, in <module>
    from scipy import full, matrix # type: ignore
ImportError: cannot import name 'full' from 'scipy' (/import/tegern-data/ulrich/MyLibs/mambaforge3/lib/python3.10/site-packages/scipy/__init__.py)
Traceback (most recent call last):
  File "/export/dump/ulrich/trash/SeisSol/generated_code/generate.py", line 182, in <module>
    generator.generate(outputDir=cmdLineArgs.outputDir,
  File "/export/dump/ulrich/trash/SeisSol/generated_code/yateto/generator.py", line 378, in generate
    cache.generate(header, fRoutines.cpp, fGpulikeRoutines.cpp)
  File "/export/dump/ulrich/trash/SeisSol/generated_code/yateto/codegen/cache.py", line 39, in generate
    declaration = generator(name, cppFileName)
  File "/export/dump/ulrich/trash/SeisSol/generated_code/yateto/codegen/gemm/gemmgen.py", line 323, in __call__
    self._callGenerator(argList)
  File "/export/dump/ulrich/trash/SeisSol/generated_code/yateto/codegen/gemm/gemmgen.py", line 231, in _callGenerator
    raise RuntimeError(f"""GEMM code generator executable "{self._cmd}" failed. Thus, the kernel generation may be incomplete.
RuntimeError: GEMM code generator executable "/import/tegern-data/ulrich/MyLibs/mambaforge3/bin/pspamm-generator" failed. Thus, the kernel generation may be incomplete.
Given command: /import/tegern-data/ulrich/MyLibs/mambaforge3/bin/pspamm-generator 20 1 20 20 20 20 generic 0 --arch hsw --prefetching pfsigonly --output_funcname pspamm_m20_n1_k20_ldA20_ldB20_ldC20_alphageneric_beta0_alignedA1_alignedC1_transAFalse_transBFalse_pfsigonly --output_filename /export/dump/ulrich/trash/SeisSol/build/src/generated_code/subroutine.cpp --precision D

EDIT: works with scipy 1.11.0

ERROR: No matching distribution found for setuptools>=61.0.0 when trying to install pspamm on supermuc

di73yeq4@login02:/hppfs/work/pn49ha/di73yeq4/seissol-spack-aid/spack/packages> module list
Currently Loaded Modulefiles:
 1) admin/1.0     3) lrz/1.0        5) intel-oneapi-compilers/2021.4.0(default:intel)   7) intel-mpi/2019-intel   9) cmake/3.21.4            11) user_spack/23.1.0       
 2) tempdir/1.0   4) spack/22.2.1   6) intel-mkl/2020                                   8) gcc/11.2.0            10) numactl/2.0.14-intel21  12) python/3.8.11-extended  

Key:
(symbolic-version)  default-version  sticky

di73yeq4@login02:/hppfs/work/pn49ha/di73yeq4/seissol-spack-aid/spack/packages> pip install --upgrade setuptools --user --proxy http://localhost:24382/
Requirement already satisfied: setuptools in /dss/lrzsys/sys/spack/release/22.2.1/views/python/._3.8.11-extended/o7ub5bgyat4qjtrqusu363fom6gg6hmv/lib/python3.8/site-packages (57.4.0)
Collecting setuptools
  Downloading setuptools-69.2.0-py3-none-any.whl.metadata (6.3 kB)
Downloading setuptools-69.2.0-py3-none-any.whl (821 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 821.5/821.5 kB 6.3 MB/s eta 0:00:00
Installing collected packages: setuptools
Successfully installed setuptools-69.2.0
2024-03-22 14:46:42,743 - pid:459704 [I] server.access_log:384 - 127.0.0.1:45664 - CONNECT files.pythonhosted.org:443 - 835185 bytes - 1514.00ms
                                                                                                                                                2024-03-22 14:46:42,744 - pid:459715 [I] server.access_log:384 - 127.0.0.1:45652 - CONNECT pypi.org:443 - 177362 bytes - 1903.68ms
                                                                 di73yeq4@login02:/hppfs/work/pn49ha/di73yeq4/seissol-spack-aid/spack/packages> pip install --upgrade setuptools --user --proxy http://localhost:git+https://github.com/SeisSol/PSpaMM.git                                      
di73yeq4@login02:/hppfs/work/pn49ha/di73yeq4/seissol-spack-aid/spack/packages> pip install git+https://github.com/SeisSol/PSpaMM.git --user --proxy http://localhost:24382/
Collecting git+https://github.com/SeisSol/PSpaMM.git
  Cloning https://github.com/SeisSol/PSpaMM.git to /hppfs/scratch/0A/di73yeq4/tmp/pip-req-build-gg_ja47x
  Running command git clone --filter=blob:none --quiet https://github.com/SeisSol/PSpaMM.git /hppfs/scratch/0A/di73yeq4/tmp/pip-req-build-gg_ja47x
  @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
  @    WARNING: REMOTE HOST IDENTIFICATION HAS CHANGED!     @
  @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
  IT IS POSSIBLE THAT SOMEONE IS DOING SOMETHING NASTY!
  Someone could be eavesdropping on you right now (man-in-the-middle attack)!
  It is also possible that a host key has just been changed.
  The fingerprint for the RSA key sent by the remote host is
  SHA256:uNiVztksCsDhcc0u9e8BujQXVUpKZIDTMczCvj3tD2s.
  Please contact your system administrator.
  Add correct host key in /dss/dsshome1/0A/di73yeq4/.ssh/known_hosts to get rid of this message.
  Offending RSA key in /dss/dsshome1/0A/di73yeq4/.ssh/known_hosts:4
  You can use following command to remove the offending key:
  ssh-keygen -R [localhost]:24380 -f /dss/dsshome1/0A/di73yeq4/.ssh/known_hosts
  Password authentication is disabled to avoid man-in-the-middle attacks.
  Keyboard-interactive authentication is disabled to avoid man-in-the-middle attacks.
Enter passphrase for key '/dss/dsshome1/0A/di73yeq4/.ssh/id_rsa': 
  @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
  @    WARNING: REMOTE HOST IDENTIFICATION HAS CHANGED!     @
  @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
  IT IS POSSIBLE THAT SOMEONE IS DOING SOMETHING NASTY!
  Someone could be eavesdropping on you right now (man-in-the-middle attack)!
  It is also possible that a host key has just been changed.
  The fingerprint for the RSA key sent by the remote host is
  SHA256:uNiVztksCsDhcc0u9e8BujQXVUpKZIDTMczCvj3tD2s.
  Please contact your system administrator.
  Add correct host key in /dss/dsshome1/0A/di73yeq4/.ssh/known_hosts to get rid of this message.
  Offending RSA key in /dss/dsshome1/0A/di73yeq4/.ssh/known_hosts:4
  You can use following command to remove the offending key:
  ssh-keygen -R [localhost]:24380 -f /dss/dsshome1/0A/di73yeq4/.ssh/known_hosts
  Password authentication is disabled to avoid man-in-the-middle attacks.
  Keyboard-interactive authentication is disabled to avoid man-in-the-middle attacks.
Enter passphrase for key '/dss/dsshome1/0A/di73yeq4/.ssh/id_rsa': 
  Resolved https://github.com/SeisSol/PSpaMM.git to commit 0f56877a0968e0aada63fcf80730cec8faa13fbc
  Installing build dependencies ... error
  error: subprocess-exited-with-error
  
  × pip subprocess to install build dependencies did not run successfully.
  │ exit code: 1
  ╰─> [7 lines of output]
      WARNING: Retrying (Retry(total=4, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError('<pip._vendor.urllib3.connection.HTTPSConnection object at 0x7f4f172cf0a0>: Failed to establish a new connection: [Errno 101] Network is unreachable')': /simple/setuptools/
      WARNING: Retrying (Retry(total=3, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError('<pip._vendor.urllib3.connection.HTTPSConnection object at 0x7f4f1730bf10>: Failed to establish a new connection: [Errno 101] Network is unreachable')': /simple/setuptools/
      WARNING: Retrying (Retry(total=2, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError('<pip._vendor.urllib3.connection.HTTPSConnection object at 0x7f4f173332e0>: Failed to establish a new connection: [Errno 101] Network is unreachable')': /simple/setuptools/
      WARNING: Retrying (Retry(total=1, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError('<pip._vendor.urllib3.connection.HTTPSConnection object at 0x7f4f172cf3a0>: Failed to establish a new connection: [Errno 101] Network is unreachable')': /simple/setuptools/
      WARNING: Retrying (Retry(total=0, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError('<pip._vendor.urllib3.connection.HTTPSConnection object at 0x7f4f172cf550>: Failed to establish a new connection: [Errno 101] Network is unreachable')': /simple/setuptools/
      ERROR: Could not find a version that satisfies the requirement setuptools>=61.0.0 (from versions: none)
      ERROR: No matching distribution found for setuptools>=61.0.0
      [end of output]
  
  note: This error originates from a subprocess, and is likely not a problem with pip.
error: subprocess-exited-with-error

× pip subprocess to install build dependencies did not run successfully.
│ exit code: 1
╰─> See above for output.

note: This error originates from a subprocess, and is likely not a problem with pip.

pspamm is still not installing the wheel requirement on the latest version

Just tested by Claudia