Incompatibility between MKL and libgomp.so.1 library

DavidD · 2021-10-19 09:50:01

Hi everyone,

i am trying to install Code_Aster on Ubuntu 20.04 with a conda environnement and i have trouble in doing so.

Please, find enclosed my log file

Here is my conda environnement

name: asterenv
channels:
- conda-forge
- defaults
dependencies:
- _libgcc_mutex=0.1=main
- _openmp_mutex=4.5=1_gnu
- blas=1.0=mkl
- boost=1.76.0=py38hfc89cab_0
- boost-cpp=1.76.0=h312852a_1
- bzip2=1.0.8=h7f98852_4
- ca-certificates=2021.10.8=ha878542_0
- certifi=2021.10.8=py38h578d9bd_0
- icu=68.1=h58526e2_0
- intel-openmp=2021.3.0=h06a4308_3350
- ld_impl_linux-64=2.35.1=h7274673_9
- libffi=3.3=he6710b0_2
- libgcc-ng=9.3.0=h5101ec6_17
- libgomp=9.3.0=h5101ec6_17
- libstdcxx-ng=9.3.0=hd4cf53a_17
- lz4-c=1.9.3=h9c3ff4c_1
- mkl=2021.3.0=h06a4308_520
- mkl-service=2.4.0=py38h7f8727e_0
- mkl_fft=1.3.0=py38h42c9631_2
- mkl_random=1.2.2=py38h51133e4_0
- ncurses=6.2=he6710b0_1
- numpy=1.21.2=py38h20f2e39_0
- numpy-base=1.21.2=py38h79a1101_0
- openssl=1.1.1l=h7f8727e_0
- pip=21.2.4=py38h06a4308_0
- python=3.8.12=h12debd9_0
- python_abi=3.8=2_cp38
- readline=8.1=h27cfd23_0
- setuptools=58.0.4=py38h06a4308_0
- six=1.16.0=pyhd3eb1b0_0
- sqlite=3.36.0=hc218d9a_0
- tk=8.6.11=h1ccaba5_0
- wheel=0.37.0=pyhd3eb1b0_1
- xz=5.2.5=h7b6447c_0
- zlib=1.2.11=h7b6447c_3
- zstd=1.5.0=ha95c52a_0

Here are the last lines of the log file

--------------------------------------------------------------------------------
SUMMARY OF INSTALLATION
--------------------------------------------------------------------------------

Installation of : hdf5 1.10.3
Destination : /home/ddanan/HSAProject/CodeAster/public/hdf5-1.10.3
Elapsed time : 904.16 s
[ OK ]
Installation of : med 4.0.0
Destination : /home/ddanan/HSAProject/CodeAster/public/med-4.0.0
Elapsed time : 729.07 s
[ OK ]
Installation of : scotch 6.0.4
Destination : /home/ddanan/HSAProject/CodeAster/public/scotch-6.0.4
Elapsed time : 250.15 s
[ OK ]
Installation of : astk 2020.0
Destination : /home/ddanan/HSAProject/CodeAster/lib/python3.8/site-packages
Elapsed time : 6.40 s
[ OK ]
Installation of : metis 5.1.0
Destination : /home/ddanan/HSAProject/CodeAster/public/metis-5.1.0
Elapsed time : 64.47 s
[ OK ]
Installation of : tfel 3.2.1
Destination : /home/ddanan/HSAProject/CodeAster/public/tfel-3.2.1
Elapsed time : 1871.75 s
[ OK ]
Installation of : mumps 5.1.2
Destination : /home/ddanan/HSAProject/CodeAster/public/mumps-5.1.2
Elapsed time : 1175.32 s
[ OK ]
Installation of : homard 11.12
Destination : /home/ddanan/HSAProject/CodeAster/public/homard-11.12
Elapsed time : 15.34 s
[ OK ]
Installation of : aster 14.6.0
Destination : /home/ddanan/HSAProject/CodeAster
Elapsed time : 1970.51 s

*** Exception None raised : None
See detailed traceback in the logfile
[FAILED]
Exit code : 4
Installation of : Code_Aster + 9 of its prerequisites
Destination : /home/ddanan/HSAProject/CodeAster
Elapsed time : 7068.99 s
[ OK ]

And next, here is the part i am concerned about in the log

Waf: Leaving directory `/tmp/install_aster.337352/aster-14.6.0/build/std/release'
+ build the elements catalog elem.1 using installed aster (from /tmp/install_aster.337352/aster-14.6.0/build/std/release/catalo/cata_ele.ojb)
stdout:
stderr: Error: mkl-service + Intel(R) MKL: MKL_THREADING_LAYER=INTEL is incompatible with libgomp.so.1 library.
Try to import numpy first or set the threading layer accordingly. Set MKL_SERVICE_FORCE_INTEL to force it.

I found several topics about this subject that invovles changing some environnement variables but it did not work.
Any idea? Is there anything wrong/strange in the log?
Thanks in advance for your help

David.

Attachments:
setup.log, Size: 1.38 MiB, Downloads: 750

DavidD · 2021-10-20 09:06:11

I guess i found the solution.

In fact, defining an environnement variable DOES work. I just did

export MKL_SERVICE_FORCE_INTEL=1

before running the setup script again.

Now i am running the sequential tests to assess whether it does work.
If it does, i will change the topic title to solve.

#1 2021-10-19 09:50:01

Incompatibility between MKL and libgomp.so.1 library

#2 2021-10-20 09:06:11

Re: Incompatibility between MKL and libgomp.so.1 library

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