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facs mpi4py install issue #53
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Hi @djgroen This was the issue regarding mpi4py that I was talking about last week... Please have a look when you have some time... |
Hi All Are you getting this error ? (you did not put the full error output) error: Python.h: No such file or directory Are you using virtual Env or Conda? Or try to call pip without any virtual env ? Could you please locate pip install --global-option="-I/home/users/xyz/include/" mpi4py the other possibility is you haven't properly installed the header files and static libraries for python dev |
Hi all. I think this is a local deployment issue. I see openmpi being installed in the setup script, but then a call to mpich in the final line of the installation script. Perhaps an important first step is that you have either openmpi or mpich set up on your machine, but not a blend of both :). Hope this help as well, in addition to @arabnejad 's very solid advice! |
output.txt I am installing in virtual Env. |
@shakir507 Could you please check if you have > dpkg -l | grep "python3-dev"
ii libpython3-dev:amd64 3.10.6-1~22.04 amd64 header files and a static library for Python (default)
ii python3-dev 3.10.6-1~22.04 amd64 header files and a static library for Python (default) |
or you can use > dpkg-query -s python3-dev
# output will be something like
Package: python3-dev
Status: install ok installed
Priority: optional
Section: python
Installed-Size: 145
Maintainer: Ubuntu Developers <ubuntu-devel-discuss@lists.ubuntu.com>
Architecture: amd64
Multi-Arch: allowed
Source: python3-defaults
Version: 3.10.6-1~22.04
Replaces: python3 (<< 3.9.2-1~), python3.1 (<< 3.1.2+20100706-3)
Depends: python3 (= 3.10.6-1~22.04), libpython3-dev (= 3.10.6-1~22.04), python3.10-dev (>= 3.10.6-1~), python3-distutils (>= 3.10.6-1~), libjs-sphinxdoc (>= 4.3)
Breaks: python3 (<< 3.9.2-1~)
Description: header files and a static library for Python (default)
Header files, a static library and development tools for building
Python modules, extending the Python interpreter or embedding Python
in applications.
.
This package is a dependency package, which depends on Debian's default
Python 3 version's headers (currently v3.10).
Original-Maintainer: Matthias Klose <doko@debian.org>
Built-Using: sphinx (= 4.3.2-1)
Homepage: https://www.python.org/ |
The anaconda environment was an issue. Couldn't get my head around that one so finally removed it. This step got the installation working as it should. |
Dear Dr Derek Groen,
I am Shakir Bilal working at University of South Florida, In Tampa. Our group has been working on a C++ based ABM simulator and seeks to perform sensistvty analysis using the facs tool that you have developed. I have been working with Dr Arindam Saha while he was here at USF last year.
The current issue is with installing the facs on my machine with python 3.8.10 on Ubuntu. The installation process is stuck with the following two issues:
`
allgatherv.c: In function ‘MPI_Allgatherv’:
allgatherv.c:50:1: internal compiler error: in init_alias_analysis, at alias.c:3468
50 | }
| ^
allgatherv.c:50:1: internal compiler error: Segmentation fault
0x7fba204e408f ???
/build/glibc-wuryBv/glibc-2.31/signal/../sysdeps/unix/sysv/linux/x86_64/sigaction.c:0
gcc: internal compiler error: Segmentation fault signal terminated program cc1
Please submit a full bug report,
with preprocessed source if appropriate.
See file:///usr/share/doc/gcc-9/README.Bugs for instructions.
make[2]: *** [Makefile:1876: allgatherv.lo] Error 1
make[2]: Leaving directory '/home/shakir/Downloads/openmpi-4.1.2/ompi/contrib/libompitrace'
make[1]: *** [Makefile:3555: all-recursive] Error 1
make[1]: Leaving directory '/home/shakir/Downloads/openmpi-4.1.2/ompi'
make: *** [Makefile:1901: all-recursive] Error 1
Collecting mpi4py
Using cached mpi4py-3.1.5.tar.gz (2.5 MB)
Installing build dependencies ... done
Getting requirements to build wheel ... done
Preparing metadata (pyproject.toml) ... done
Building wheels for collected packages: mpi4py
Building wheel for mpi4py (pyproject.toml) ... error
error: subprocess-exited-with-error
× Building wheel for mpi4py (pyproject.toml) did not run successfully.
│ exit code: 1
╰─> [242 lines of output]
'
2)
'
#include "Python.h"
^~~~~~~~~~
compilation terminated.
error: command '/home/shakir/sfw/MPICH/bin/mpicc' failed with exit code 1
[end of output]
note: This error originates from a subprocess, and is likely not a problem with pip.
ERROR: Failed building wheel for mpi4py
Failed to build mpi4py
ERROR: Could not build wheels for mpi4py, which is required to install pyproject.toml-based projects'
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