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License: BSD 3-Clause "New" or "Revised" License
A conda-smithy repository for mumps.
License: BSD 3-Clause "New" or "Revised" License
The fix in #88 is creating problems, even if i solved the crash in import kwant; kwant.test()
.
See #87 (comment) for more details.
.
.
after merging mumps-mpi into the main recipe in #36, we have a copy of the examples
directory (with a very slightly modified Makefile) in the recipe. We don't need to carry these files around because we can use
test:
source_files:
- examples
to get the example sources into the test environment.
I started trying to do this in #36 but had a hell of a time with little edge cases and didn't want to hold up that PR anymore while CI turnaround is so slow. We should be able to do this in a standalone PR without any changes to how things are actually built.
I was hoping to get OpenMP working with the win64 conda-forge mumps module:
mumps 5.1.2 h8933c1f_1001 conda-forge
The verbose output for the mumps module shows the build is without OMP
. If I manually build with compiler openmp flags the output shows #OMP = 8
. The openmp build runs 2-3x faster for larger problems on my 4-core laptop, so it is definitely worthwhile.
I am working on a PR to enable OpenMP but find the mumps-feedstock is using NMake Makefiles and flang for win64, rather than MinGW Makefiles and gfortran. (Not sure why I don't get the flang build when I use conda install mumps
?)
I can build the module from the feedstock using flang, but flang gives command failed due to signal
if I add the -mp
openmp compile flag. I have not found any relevant LLVM/MSVC openmp support info/limitiations, but clang works fine for an C openmp code.
The linux build with openmp is fine.
Should I do a PR for a MinGW/gfortran build, or any suggestions on getting OpenMP working with flang?
People need MUMPS built with MPI for use in PETSc, and I'm trying to figure out the best way to go about it. Would it be possible for this recipe to be built with MPI? Or should that be done as a separate mumps-mpi
package? Is there a downside to having built with MPI when running in serial?
If it should be a separate package that can be done on this repo in a branch (as is done with scotch/pt-scotch), or a new feedstock. Preferences?
See https://anaconda.org/conda-forge/mumps-mpi/files.
This is due to the mumps-mpi package having the same hash for the two variants.
Mumps is currently at version 5.5.1, but version 5.2.1 is the latest version available from conda-forge. Would it be possible to update to a more recent version?
Issue:
Both the sequential version and the mpi version install libraries with the same name, e.g. libdmumps.a. If both versions are installed, the later installed versions overwrites the other one.
Since the mumps libraries are static, this does not affect other conda packages at this point, as they will be already linked statically to the right version at installation time. However, if you want to use them directly in your code, this is a problem.
I would suggest to use different names for the two versions, like Debian does (see https://tracker.debian.org/pkg/mumps and related pages).
@conda-forge-admin, please add user @traversaro
Currently, this recipe builds mumps as a static library. As such, it contains
undefined symbols that are supposed to be found in the libraries that mumps
depends on (e.g. scotch).
The problem with this is that whenever we want to link against mumps we also have to link against all the dependencies of mumps as well (see e.g. this thread). This is clearly not great.
Debian already builds a mumps as a shared library, and as far as I can tell it is just a case of applying a few patches to the makefiles to add extra targets that correctly invoke the compiler to build shared libs.
I think that it may just be a case of taking over these patches from the Debian packaging (available over here) and massaging them slightly (e.g. to template out the library version).
Both the Metis and libscotch packages are available through conda-forge on windows. Is there any interest in getting the windows mumps distribution built against these?
I might have a little bit of time to play with getting them added to the cmake scripts, but I'm sure other's might be able to do this faster as I'm still fairly novice at creating cmake scripts.
Need to update with BLAS stuff we should be following these guidelines. Can also look at NumPy and SciPy for examples. Also please remember to create the PR from a branch on your fork.
I would like to put in a request for installed pkgconfig files for the installed mumps. I don't imagine that the source code generates anything, but you could create some simple files for the libraries installed during the conda-forge building steps. As a simple example:
prefix= <-WRITE $PREFIX TO HERE DURING BUILD
exec_prefix=${prefix}
libdir=${prefix}/lib
sharedlibdir=${libdir}
includedir=${prefix}/include
Name: dmumps_seq
Description: The sequential double MUMPS library
Version: <- WRITE THE VERSION STRING TO HERE DURING BUILD
Cflags: -I${includedir}
Libs: -L${libdir} -ldmumps_seq
I also do not know what this would correspond to on windows machines.
Here is one error:
C:\Miniconda\Scripts\conda.exe install python=3.6 conda-build conda conda-forge::conda-forge-ci-setup=2 --quiet --yes -c conda-forge
(node:3812) Warning: Use Cipheriv for counter mode of aes-256-ctr
(node:3812) Warning: Use Cipheriv for counter mode of aes-256-ctr
(node:3812) Warning: Use Cipheriv for counter mode of aes-256-ctr
(node:3812) Warning: Use Cipheriv for counter mode of aes-256-ctr
(node:3812) Warning: Use Cipheriv for counter mode of aes-256-ctr
(node:3812) Warning: Use Cipheriv for counter mode of aes-256-ctr
(node:3812) Warning: Use Cipheriv for counter mode of aes-256-ctr
(node:3812) Warning: Use Cipheriv for counter mode of aes-256-ctr
(node:3812) Warning: Use Cipheriv for counter mode of aes-256-ctr
(node:3812) Warning: Use Cipheriv for counter mode of aes-256-ctr
Collecting package metadata: ...working... done
Solving environment: ...working... done
## Package Plan ##
environment location: C:\Miniconda
added / updated specs:
- conda
- conda-build
- conda-forge::conda-forge-ci-setup=2
- python=3.6
The following packages will be downloaded:
package | build
---------------------------|-----------------
anaconda-client-1.7.2 | py_0 69 KB conda-forge
asn1crypto-1.3.0 | py36_0 159 KB conda-forge
attrs-19.3.0 | py_0 35 KB conda-forge
beautifulsoup4-4.8.2 | py36_0 159 KB conda-forge
bzip2-1.0.8 | hfa6e2cd_2 148 KB conda-forge
Running `conda clean --packages` may resolve your problem.
##[error]Failed to install packages. Error: C:\Miniconda\Scripts\conda.exe failed with return code: 1
Finishing: Install conda-build and activate environment
The latest version of mumps-include
seems to miss a header file. Specifically, mumps_c_types.h
from mumps-include
has these lines:
/* mumps_int_def.h will define either MUMPS_INTSIZE32 (default)
or MUMPS_INTSIZE64 (if compilation is with -DINTSIZE64 to
match Fortran -i8 or equivalent option). This allows one to
test from an external code whether MUMPS_INT is 64bits or not */
#include "mumps_int_def.h"
however mumps_int_def.h
is missing from mumps-include
.
mumps-include 5.6.2 ha770c72_0 conda-forge
mumps-seq 5.6.2 h5c37537_0 conda-forge
-
On Windows, the mumps-seq
package installs the files:
cmumps.lib
dmumps.lib
smumps.lib
zmumps.lib
in the Library\bin\
directory, instead of the Library\lib
directory in which .lib files are usually installed.
conda list
):
$ conda list
(ipopt-tests) C:\src\ipopt-tests\Ipopt\build-nmake>conda list
# packages in environment at C:\Users\STraversaro\Miniconda3\envs\ipopt-tests:
#
# Name Version Build Channel
c-compiler 1.1.1 he774522_1 conda-forge
clangdev 5.0.0 flang_3 [flang] conda-forge
cmake 3.18.3 h39d44d4_0 conda-forge
compilers 1.1.1 1 conda-forge
cxx-compiler 1.1.1 h74a9793_1 conda-forge
flang 5.0.0 he025d50_20180525 conda-forge
flang_win-64 5.0.0 20180525 conda-forge
fortran-compiler 1.1.1 he67e8c7_1 conda-forge
gettext 0.19.8.1 hfbb10ce_1004 conda-forge
intel-openmp 2020.2 254
lapack 3.9.0 netlib conda-forge
libblas 3.9.0 2_h8933c1f_netlib conda-forge
libffi 3.2.1 ha925a31_1007 conda-forge
libflang 5.0.0 h6538335_20180525 conda-forge
libglib 2.66.2 h35efcdc_0 conda-forge
libiconv 1.16 he774522_0 conda-forge
liblapack 3.9.0 2_h8933c1f_netlib conda-forge
llvm-meta 5.0.0 0 conda-forge
m2w64-gcc-libgfortran 5.3.0 6
m2w64-gcc-libs 5.3.0 7
m2w64-gcc-libs-core 5.3.0 7
m2w64-gmp 6.1.0 2
m2w64-libwinpthread-git 5.0.0.4634.697f757 2
mkl 2020.2 256
msys2-conda-epoch 20160418 1
mumps-seq 5.2.1 h0f4c095_9 conda-forge
ninja 1.10.1 h587dcfd_2 conda-forge
openmp 5.0.0 vc14_1 conda-forge
pcre 8.44 ha925a31_0 conda-forge
pkg-config 0.29.2 h4a39e8b_1008 conda-forge
vc 14.1 h869be7e_1 conda-forge
vs2015_runtime 14.16.27012 h30e32a0_2 conda-forge
vs2017_win-64 19.16.27038 h2e3bad8_2 conda-forge
vswhere 2.7.1 h21ff451_0
zlib 1.2.11 h62dcd97_1010 conda-forge
(ipopt-tests) C:\src\ipopt-tests\Ipopt\build-nmake>
conda
and system ( conda info
):
$ conda info
(ipopt-tests) C:\src\ipopt-tests\Ipopt\build-nmake>conda info
active environment : ipopt-tests
active env location : C:\Users\STraversaro\Miniconda3\envs\ipopt-tests
shell level : 2
user config file : C:\Users\STraversaro\.condarc
populated config files : C:\Users\STraversaro\.condarc
conda version : 4.8.3
conda-build version : not installed
python version : 3.8.3.final.0
virtual packages : __cuda=10.2
base environment : C:\Users\STraversaro\Miniconda3 (writable)
channel URLs : https://conda.anaconda.org/conda-forge/win-64
https://conda.anaconda.org/conda-forge/noarch
https://repo.anaconda.com/pkgs/main/win-64
https://repo.anaconda.com/pkgs/main/noarch
https://repo.anaconda.com/pkgs/r/win-64
https://repo.anaconda.com/pkgs/r/noarch
https://repo.anaconda.com/pkgs/msys2/win-64
https://repo.anaconda.com/pkgs/msys2/noarch
package cache : C:\Users\STraversaro\Miniconda3\pkgs
C:\Users\STraversaro\.conda\pkgs
C:\Users\STraversaro\AppData\Local\conda\conda\pkgs
envs directories : C:\Users\STraversaro\Miniconda3\envs
C:\Users\STraversaro\.conda\envs
C:\Users\STraversaro\AppData\Local\conda\conda\envs
platform : win-64
user-agent : conda/4.8.3 requests/2.23.0 CPython/3.8.3 Windows/10 Windows/10.0.19041
administrator : False
netrc file : None
offline mode : False
(ipopt-tests) C:\src\ipopt-tests\Ipopt\build-nmake>
when trying to link with IPOPT (conda-forge/staged-recipes#1607), I'm getting errors on not including mpi.h
. It looks like this is supposed to get included with mumps
, but the current recipe seems to omit it: http://list.coin-or.org/pipermail/ipopt/2013-June/003410.html
I'll send in a PR to include it, but do we need to worry about conflicting with mpi.h
from any other packages?
I've been attempting to build a package that dynamically links against the sequential library and running into several issues.
The first is related to #102, which looks to already have a PR open.
For context, I'm running on an OSX arm processor.
After a temporary workaround of removing that import, successfully compiling and linking together the package, I now run into issues at runtime. It is unable to find the library at runtime. Using otool -L libdmumps_seq.dylib
(on this installed libraries from conda-forge) reveals the following:
../lib/libdmumps_seq.dylib (compatibility version 0.0.0, current version 0.0.0)
@rpath/libmetis.dylib (compatibility version 0.0.0, current version 0.0.0)
@rpath/libmpiseq_seq.dylib (compatibility version 0.0.0, current version 0.0.0)
@rpath/liblapack.3.dylib (compatibility version 0.0.0, current version 0.0.0)
@rpath/libblas.3.dylib (compatibility version 0.0.0, current version 0.0.0)
@rpath/libmumps_common_seq.dylib (compatibility version 0.0.0, current version 0.0.0)
@rpath/libgfortran.5.dylib (compatibility version 6.0.0, current version 6.0.0)
/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.0.0)
It would appear that the rpath
is not set for the first entry of the library (the other libraries smumps_seq
, cmumps_seq
, zmumps_seq
have this same issue). However libesmumps.dylib
and libmumps_common_seq.dylib
do not have this issue.
anyio 4.2.0 pyhd8ed1ab_0 conda-forge
appnope 0.1.3 pyhd8ed1ab_0 conda-forge
argon2-cffi 23.1.0 pyhd8ed1ab_0 conda-forge
argon2-cffi-bindings 21.2.0 py311heffc1b2_4 conda-forge
arrow 1.3.0 pyhd8ed1ab_0 conda-forge
asttokens 2.4.1 pyhd8ed1ab_0 conda-forge
async-lru 2.0.4 pyhd8ed1ab_0 conda-forge
attrs 23.1.0 pyh71513ae_1 conda-forge
babel 2.14.0 pyhd8ed1ab_0 conda-forge
beautifulsoup4 4.12.2 pyha770c72_0 conda-forge
bleach 6.1.0 pyhd8ed1ab_0 conda-forge
brotli 1.1.0 hb547adb_1 conda-forge
brotli-bin 1.1.0 hb547adb_1 conda-forge
brotli-python 1.1.0 py311ha891d26_1 conda-forge
bzip2 1.0.8 h93a5062_5 conda-forge
ca-certificates 2023.11.17 hf0a4a13_0 conda-forge
cached-property 1.5.2 hd8ed1ab_1 conda-forge
cached_property 1.5.2 pyha770c72_1 conda-forge
certifi 2023.11.17 pyhd8ed1ab_0 conda-forge
cffi 1.16.0 py311h4a08483_0 conda-forge
charset-normalizer 3.3.2 pyhd8ed1ab_0 conda-forge
colorama 0.4.6 pyhd8ed1ab_0 conda-forge
comm 0.1.4 pyhd8ed1ab_0 conda-forge
contourpy 1.2.0 py311hd03642b_0 conda-forge
cycler 0.12.1 pyhd8ed1ab_0 conda-forge
cython 3.0.7 py311h92babd0_0 conda-forge
debugpy 1.8.0 py311ha891d26_1 conda-forge
decorator 5.1.1 pyhd8ed1ab_0 conda-forge
defusedxml 0.7.1 pyhd8ed1ab_0 conda-forge
discretize 0.10.0 py311hc00d0f6_1 conda-forge
entrypoints 0.4 pyhd8ed1ab_0 conda-forge
exceptiongroup 1.2.0 pyhd8ed1ab_0 conda-forge
executing 2.0.1 pyhd8ed1ab_0 conda-forge
fonttools 4.47.0 py311h05b510d_0 conda-forge
fqdn 1.5.1 pyhd8ed1ab_0 conda-forge
freetype 2.12.1 hadb7bae_2 conda-forge
gettext 0.21.1 h0186832_0 conda-forge
idna 3.6 pyhd8ed1ab_0 conda-forge
importlib-metadata 7.0.0 pyha770c72_0 conda-forge
importlib_metadata 7.0.0 hd8ed1ab_0 conda-forge
importlib_resources 6.1.1 pyhd8ed1ab_0 conda-forge
ipykernel 6.26.0 pyh3cd1d5f_0 conda-forge
ipython 8.18.1 pyh707e725_3 conda-forge
ipywidgets 8.1.1 pyhd8ed1ab_0 conda-forge
isoduration 20.11.0 pyhd8ed1ab_0 conda-forge
jedi 0.19.1 pyhd8ed1ab_0 conda-forge
jinja2 3.1.2 pyhd8ed1ab_1 conda-forge
json5 0.9.14 pyhd8ed1ab_0 conda-forge
jsonpointer 2.4 py311h267d04e_3 conda-forge
jsonschema 4.20.0 pyhd8ed1ab_0 conda-forge
jsonschema-specifications 2023.11.2 pyhd8ed1ab_0 conda-forge
jsonschema-with-format-nongpl 4.20.0 pyhd8ed1ab_0 conda-forge
jupyter 1.0.0 pyhd8ed1ab_10 conda-forge
jupyter-lsp 2.2.1 pyhd8ed1ab_0 conda-forge
jupyter_client 8.6.0 pyhd8ed1ab_0 conda-forge
jupyter_console 6.6.3 pyhd8ed1ab_0 conda-forge
jupyter_core 5.5.1 py311h267d04e_0 conda-forge
jupyter_events 0.9.0 pyhd8ed1ab_0 conda-forge
jupyter_server 2.12.1 pyhd8ed1ab_0 conda-forge
jupyter_server_terminals 0.5.0 pyhd8ed1ab_0 conda-forge
jupyterlab 4.0.9 pyhd8ed1ab_0 conda-forge
jupyterlab_pygments 0.3.0 pyhd8ed1ab_0 conda-forge
jupyterlab_server 2.25.2 pyhd8ed1ab_0 conda-forge
jupyterlab_widgets 3.0.9 pyhd8ed1ab_0 conda-forge
kiwisolver 1.4.5 py311he4fd1f5_1 conda-forge
lcms2 2.16 ha0e7c42_0 conda-forge
lerc 4.0.0 h9a09cb3_0 conda-forge
libblas 3.9.0 20_osxarm64_accelerate conda-forge
libbrotlicommon 1.1.0 hb547adb_1 conda-forge
libbrotlidec 1.1.0 hb547adb_1 conda-forge
libbrotlienc 1.1.0 hb547adb_1 conda-forge
libcblas 3.9.0 20_osxarm64_accelerate conda-forge
libcxx 16.0.6 h4653b0c_0 conda-forge
libdeflate 1.19 hb547adb_0 conda-forge
libexpat 2.5.0 hb7217d7_1 conda-forge
libffi 3.4.2 h3422bc3_5 conda-forge
libgfortran 5.0.0 13_2_0_hd922786_1 conda-forge
libgfortran5 13.2.0 hf226fd6_1 conda-forge
libglib 2.78.3 hb438215_0 conda-forge
libiconv 1.17 h0d3ecfb_2 conda-forge
libjpeg-turbo 3.0.0 hb547adb_1 conda-forge
liblapack 3.9.0 20_osxarm64_accelerate conda-forge
libpng 1.6.39 h76d750c_0 conda-forge
libscotch 7.0.4 hc938e73_1 conda-forge
libsodium 1.0.18 h27ca646_1 conda-forge
libsqlite 3.44.2 h091b4b1_0 conda-forge
libtiff 4.6.0 ha8a6c65_2 conda-forge
libwebp-base 1.3.2 hb547adb_0 conda-forge
libxcb 1.15 hf346824_0 conda-forge
libzlib 1.2.13 h53f4e23_5 conda-forge
llvm-openmp 17.0.6 hcd81f8e_0 conda-forge
markupsafe 2.1.3 py311heffc1b2_1 conda-forge
matplotlib 3.8.2 py311ha1ab1f8_0 conda-forge
matplotlib-base 3.8.2 py311hfdba5f6_0 conda-forge
matplotlib-inline 0.1.6 pyhd8ed1ab_0 conda-forge
meson 1.3.0 pyhd8ed1ab_0 conda-forge
meson-python 0.15.0 pyh0c530f3_0 conda-forge
metis 5.1.1 h965bd2d_2 conda-forge
mistune 3.0.2 pyhd8ed1ab_0 conda-forge
mumps-include 5.6.2 hce30654_0 conda-forge
mumps-seq 5.6.2 hfe4d18a_0 conda-forge
mumpys 0.0.1 pypi_0 pypi
munkres 1.1.4 pyh9f0ad1d_0 conda-forge
nbclient 0.8.0 pyhd8ed1ab_0 conda-forge
nbconvert 7.13.0 pyhd8ed1ab_0 conda-forge
nbconvert-core 7.13.0 pyhd8ed1ab_0 conda-forge
nbconvert-pandoc 7.13.0 pyhd8ed1ab_0 conda-forge
nbformat 5.9.2 pyhd8ed1ab_0 conda-forge
ncurses 6.4 h463b476_2 conda-forge
nest-asyncio 1.5.8 pyhd8ed1ab_0 conda-forge
ninja 1.11.1 hffc8910_0 conda-forge
notebook 7.0.6 pyhd8ed1ab_0 conda-forge
notebook-shim 0.2.3 pyhd8ed1ab_0 conda-forge
numpy 1.26.2 py311h6d074dd_0 conda-forge
openjpeg 2.5.0 h4c1507b_3 conda-forge
openssl 3.2.0 h0d3ecfb_1 conda-forge
overrides 7.4.0 pyhd8ed1ab_0 conda-forge
packaging 23.2 pyhd8ed1ab_0 conda-forge
pandoc 3.1.3 hce30654_0 conda-forge
pandocfilters 1.5.0 pyhd8ed1ab_0 conda-forge
parso 0.8.3 pyhd8ed1ab_0 conda-forge
pcre2 10.42 h26f9a81_0 conda-forge
pexpect 4.8.0 pyh1a96a4e_2 conda-forge
pickleshare 0.7.5 py_1003 conda-forge
pillow 10.1.0 py311hb9c5795_0 conda-forge
pip 23.3.2 pyhd8ed1ab_0 conda-forge
pkg-config 0.29.2 hab62308_1008 conda-forge
pkgutil-resolve-name 1.3.10 pyhd8ed1ab_1 conda-forge
platformdirs 4.1.0 pyhd8ed1ab_0 conda-forge
prometheus_client 0.19.0 pyhd8ed1ab_0 conda-forge
prompt-toolkit 3.0.42 pyha770c72_0 conda-forge
prompt_toolkit 3.0.42 hd8ed1ab_0 conda-forge
psutil 5.9.7 py311h05b510d_0 conda-forge
pthread-stubs 0.4 h27ca646_1001 conda-forge
ptyprocess 0.7.0 pyhd3deb0d_0 conda-forge
pure_eval 0.2.2 pyhd8ed1ab_0 conda-forge
pyaccel 0.0.1 pypi_0 pypi
pycparser 2.21 pyhd8ed1ab_0 conda-forge
pygments 2.17.2 pyhd8ed1ab_0 conda-forge
pyobjc-core 10.1 py311h665608e_0 conda-forge
pyobjc-framework-cocoa 10.1 py311h665608e_0 conda-forge
pyparsing 3.1.1 pyhd8ed1ab_0 conda-forge
pyproject-metadata 0.7.1 pyhd8ed1ab_0 conda-forge
pysocks 1.7.1 pyha2e5f31_6 conda-forge
python 3.11.7 hdf0ec26_0_cpython conda-forge
python-dateutil 2.8.2 pyhd8ed1ab_0 conda-forge
python-fastjsonschema 2.19.0 pyhd8ed1ab_0 conda-forge
python-json-logger 2.0.7 pyhd8ed1ab_0 conda-forge
python_abi 3.11 4_cp311 conda-forge
pytz 2023.3.post1 pyhd8ed1ab_0 conda-forge
pyyaml 6.0.1 py311heffc1b2_1 conda-forge
pyzmq 25.1.2 py311h6727e71_0 conda-forge
qtconsole-base 5.5.1 pyha770c72_0 conda-forge
qtpy 2.4.1 pyhd8ed1ab_0 conda-forge
readline 8.2 h92ec313_1 conda-forge
referencing 0.32.0 pyhd8ed1ab_0 conda-forge
requests 2.31.0 pyhd8ed1ab_0 conda-forge
rfc3339-validator 0.1.4 pyhd8ed1ab_0 conda-forge
rfc3986-validator 0.1.1 pyh9f0ad1d_0 conda-forge
rpds-py 0.15.2 py311h94f323b_0 conda-forge
scipy 1.11.4 py311h2b215a9_0 conda-forge
scotch 7.0.4 heaa5b5c_1 conda-forge
send2trash 1.8.2 pyhd1c38e8_0 conda-forge
setuptools 68.2.2 pyhd8ed1ab_0 conda-forge
six 1.16.0 pyh6c4a22f_0 conda-forge
sniffio 1.3.0 pyhd8ed1ab_0 conda-forge
soupsieve 2.5 pyhd8ed1ab_1 conda-forge
stack_data 0.6.2 pyhd8ed1ab_0 conda-forge
terminado 0.18.0 pyh31c8845_0 conda-forge
tinycss2 1.2.1 pyhd8ed1ab_0 conda-forge
tk 8.6.13 h5083fa2_1 conda-forge
tomli 2.0.1 pyhd8ed1ab_0 conda-forge
tornado 6.3.3 py311heffc1b2_1 conda-forge
traitlets 5.14.0 pyhd8ed1ab_0 conda-forge
types-python-dateutil 2.8.19.14 pyhd8ed1ab_0 conda-forge
typing-extensions 4.9.0 hd8ed1ab_0 conda-forge
typing_extensions 4.9.0 pyha770c72_0 conda-forge
typing_utils 0.1.0 pyhd8ed1ab_0 conda-forge
tzdata 2023c h71feb2d_0 conda-forge
uri-template 1.3.0 pyhd8ed1ab_0 conda-forge
urllib3 2.1.0 pyhd8ed1ab_0 conda-forge
wcwidth 0.2.12 pyhd8ed1ab_0 conda-forge
webcolors 1.13 pyhd8ed1ab_0 conda-forge
webencodings 0.5.1 pyhd8ed1ab_2 conda-forge
websocket-client 1.7.0 pyhd8ed1ab_0 conda-forge
wheel 0.42.0 pyhd8ed1ab_0 conda-forge
widgetsnbextension 4.0.9 pyhd8ed1ab_0 conda-forge
xorg-libxau 1.0.11 hb547adb_0 conda-forge
xorg-libxdmcp 1.1.3 h27ca646_0 conda-forge
xz 5.2.6 h57fd34a_0 conda-forge
yaml 0.2.5 h3422bc3_2 conda-forge
zeromq 4.3.5 h965bd2d_0 conda-forge
zipp 3.17.0 pyhd8ed1ab_0 conda-forge
zlib 1.2.13 h53f4e23_5 conda-forge
zstd 1.5.5 h4f39d0f_0 conda-forge
active environment : simulation
active env location : /Users/jcapriot/miniforge3/envs/simulation
shell level : 4
user config file : /Users/jcapriot/.condarc
populated config files : /Users/jcapriot/miniforge3/.condarc
conda version : 23.3.1
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/Users/jcapriot/.conda/pkgs
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kwant
currently has no MUMPS support (even though MUMPS should do nearly ALL the heavy lifting there), I thought I had fixed it in the latest build.
We used to link against mpiseq
however that library isn't being build anymore. Linking against the MPI versions will result in errors.
Before we linked against: zmumps mumps_common pord metis esmumps scotch scotcherr gfortran
Now I did: ptesmumps ptscotch ptscotcherr mpi mpifort scalapack openblas pthread
plus all the former libs.
When linking agaist the MPI libs, kwant test error on:
Attempting to use an MPI routine before initializing MPICH
@jbweston and @michaelwimmer do you think we should build the sequential version of MUMPS again?
Related: conda-forge/kwant-feedstock#34
Metis 1.1.1 causes a segfault so a pin is needed (but even better would be a repo data patach)
mumps-seq 5.2.1 h2104b81_11 metis >=5.1.0,<5.2.0a0 conda-forge
mamba info
mamba version : 1.4.7
active environment : metis
active env location : /home/tinkerer/.conda/envs/metis
shell level : 2
user config file : /home/tinkerer/.condarc
populated config files : /opt/conda/.condarc
conda version : 23.5.0
conda-build version : not installed
python version : 3.11.4.final.0
virtual packages : __archspec=1=x86_64
__glibc=2.35=0
__linux=3.10.0=0
__unix=0=0
base environment : /opt/conda (writable)
conda av data dir : /opt/conda/etc/conda
conda av metadata url : None
channel URLs : https://conda.anaconda.org/conda-forge/linux-64
https://conda.anaconda.org/conda-forge/noarch
package cache : /home/tinkerer/.conda/pkgs
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/opt/conda/envs
platform : linux-64
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UID:GID : 1004:100
netrc file : None
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Originally reported in dolfinx-mpc, I've now reproduced the issue with just petsc4py with help from @jorgensd. Running a simple solve segfaults. Amazingly, this somehow only affects mac openmpi builds. All other combinations I've tested work fine.
And after some local rebuilds of petsc and mumps, I have narrowed this down to the shared-library builds of mumps that are the issue. When I rebuild mumps-mpi
with static libs only and then rebuild petsc with that, there are no errors.
The segfault:
* thread #1, name = 'main', queue = 'com.apple.main-thread', stop reason = EXC_BAD_ACCESS (code=1, address=0x6001550217f0)
* frame #0: 0x00000001024c98a0 libdmumps.dylib`dmumps_scatter_dist_rhs_ + 736
frame #1: 0x00000001024c4d94 libdmumps.dylib`dmumps_solve_driver_ + 56724
frame #2: 0x0000000102516a1c libdmumps.dylib`dmumps_ + 1708
frame #3: 0x000000010251b114 libdmumps.dylib`dmumps_f77_ + 4228
frame #4: 0x0000000102514ba4 libdmumps.dylib`dmumps_c + 3312
frame #5: 0x00000001030c7a90 libpetsc.3.20.3.dylib`MatSolve_MUMPS + 688
frame #6: 0x0000000102fd61d0 libpetsc.3.20.3.dylib`MatSolve + 308
frame #7: 0x000000010374bd7c libpetsc.3.20.3.dylib`PCApply_LU + 84
frame #8: 0x0000000103880710 libpetsc.3.20.3.dylib`PCApply + 204
frame #9: 0x00000001036556c4 libpetsc.3.20.3.dylib`KSPSolve_PREONLY + 248
frame #10: 0x00000001036fa518 libpetsc.3.20.3.dylib`KSPSolve_Private + 1056
frame #11: 0x00000001036fa0b4 libpetsc.3.20.3.dylib`KSPSolve + 16
frame #12: 0x00000001019aaf38 PETSc.cpython-310-darwin.so`__pyx_pw_8petsc4py_5PETSc_3KSP_101solve + 176
Still working out what to do about that, but the shared-library builds on mac rely on patches I made, so something could be wrong there.
# packages in environment at /Users/minrk/conda/envs/ompi-petsc-latest:
#
# Name Version Build Channel
bzip2 1.0.8 h93a5062_5 conda-forge
c-ares 1.26.0 h93a5062_0 conda-forge
ca-certificates 2023.11.17 hf0a4a13_0 conda-forge
fftw 3.3.10 mpi_openmpi_haef8dc3_8 conda-forge
gmp 6.3.0 h965bd2d_0 conda-forge
hdf5 1.14.3 mpi_openmpi_h20f603a_0 conda-forge
hypre 2.28.0 mpi_openmpi_haba3941_0 conda-forge
icu 73.2 hc8870d7_0 conda-forge
krb5 1.21.2 h92f50d5_0 conda-forge
libaec 1.1.2 h13dd4ca_1 conda-forge
libblas 3.9.0 21_osxarm64_openblas conda-forge
libcblas 3.9.0 21_osxarm64_openblas conda-forge
libcurl 8.5.0 h2d989ff_0 conda-forge
libcxx 16.0.6 h4653b0c_0 conda-forge
libedit 3.1.20191231 hc8eb9b7_2 conda-forge
libev 4.33 h93a5062_2 conda-forge
libffi 3.4.2 h3422bc3_5 conda-forge
libgfortran 5.0.0 13_2_0_hd922786_2 conda-forge
libgfortran5 13.2.0 hf226fd6_2 conda-forge
libhwloc 2.9.3 default_h4394839_1009 conda-forge
libiconv 1.17 h0d3ecfb_2 conda-forge
liblapack 3.9.0 21_osxarm64_openblas conda-forge
libnghttp2 1.58.0 ha4dd798_1 conda-forge
libopenblas 0.3.26 openmp_h6c19121_0 conda-forge
libptscotch 7.0.4 h820b06d_1 conda-forge
libscotch 7.0.4 hf7fe8bf_1 conda-forge
libsqlite 3.44.2 h091b4b1_0 conda-forge
libssh2 1.11.0 h7a5bd25_0 conda-forge
libxml2 2.12.4 h0d0cfa8_1 conda-forge
libzlib 1.2.13 h53f4e23_5 conda-forge
llvm-openmp 17.0.6 hcd81f8e_0 conda-forge
metis 5.1.0 h13dd4ca_1007 conda-forge
mpfr 4.2.1 h9546428_0 conda-forge
mpi 1.0 openmpi conda-forge
mpi4py 3.1.5 py310hd3bd7df_0 conda-forge
mumps-include 5.6.2 hce30654_4 conda-forge
mumps-mpi 5.6.2 hc6b315c_4 conda-forge
ncurses 6.4 h463b476_2 conda-forge
numpy 1.26.3 py310hd45542a_0 conda-forge
openmpi 4.1.6 h526c993_101 conda-forge
openssl 3.2.0 h0d3ecfb_1 conda-forge
parmetis 4.0.3 h6eb5794_1005 conda-forge
petsc 3.20.4 real_hdd9ae42_100 conda-forge
petsc4py 3.20.3 real_heb9844d_100 conda-forge
pip 23.3.2 pyhd8ed1ab_0 conda-forge
ptscotch 7.0.4 hc1c4572_1 conda-forge
python 3.10.13 h2469fbe_1_cpython conda-forge
python_abi 3.10 4_cp310 conda-forge
readline 8.2 h92ec313_1 conda-forge
scalapack 2.2.0 h515df86_1 conda-forge
scotch 7.0.4 hc1c4572_1 conda-forge
setuptools 69.0.3 pyhd8ed1ab_0 conda-forge
suitesparse 5.10.1 h79486c6_3 conda-forge
superlu 5.2.2 hc615359_0 conda-forge
superlu_dist 8.2.1 h3dacc9e_1 conda-forge
tbb 2021.11.0 h2ffa867_1 conda-forge
tk 8.6.13 h5083fa2_1 conda-forge
tzdata 2023d h0c530f3_0 conda-forge
wheel 0.42.0 pyhd8ed1ab_0 conda-forge
xz 5.2.6 h57fd34a_0 conda-forge
yaml 0.2.5 h3422bc3_2 conda-forge
zlib 1.2.13 h53f4e23_5 conda-forge
zstd 1.5.5 h4f39d0f_0 conda-forge
active environment : ompi-mumps-561
active env location : /Users/minrk/conda/envs/ompi-mumps-561
shell level : 2
user config file : /Users/minrk/.condarc
populated config files : /Users/minrk/conda/.condarc
/Users/minrk/.condarc
conda version : 23.11.0
conda-build version : 3.28.4
python version : 3.10.13.final.0
solver : libmamba (default)
virtual packages : __archspec=1=m1
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base environment : /Users/minrk/conda (writable)
conda av data dir : /Users/minrk/conda/etc/conda
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channel URLs : https://conda.anaconda.org/conda-forge/osx-arm64
https://conda.anaconda.org/conda-forge/noarch
package cache : /Users/minrk/conda/pkgs
/Users/minrk/.conda/pkgs
envs directories : /Users/minrk/conda/envs
/Users/minrk/.conda/envs
platform : osx-arm64
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UID:GID : 501:20
netrc file : /Users/minrk/.netrc
offline mode : False
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