Install new python module snapatac2

Dear HPC team,
could you please install the python module “snapatac2” (version 2.4 seems to be the latest one) on Baobab?
Thank you already so much in advance,
Anna

Hi @Anna.Ramisch

I am on it :slight_smile:

I keep you in touch !

1 Like

Dear @Anna.Ramisch,

I’m still trying to build snapatac2, but we have to rebuild a lot of dependencies with the new version of GCC, which takes time.

I haven’t forgotten you!

Dear Anna,

Unfortunately, I couldn’t install snapatac with easybuild because of an internal error in a pip package in one of its dependencies… However, you can install it in your home by following this procedure:

before launching the installation in pip :

ml GCC/12.3.0 OpenMPI CMake python-igraph

https://kzhang.org/SnapATAC2/install.html#build-from-the-latest-source-code

After the local installation it’s working for me:

(baobab)-[alberta@login2 snapatac2]$ ml

Currently Loaded Modules:
  1) EasyBuild/4.8.1

 
(baobab)-[alberta@login2 snapatac2]$  module load GCC/12.3.0 OpenMPI CMake python-igraph
(baobab)-[alberta@login2 snapatac2]$ ml

Currently Loaded Modules:
  1) EasyBuild/4.8.1   6) numactl/2.0.16     11) OpenSSL/1.1       16) UCC/1.2.0      21) libarchive/3.6.2  26) FFTW.MPI/3.3.10     31) libffi/3.4.4     36) igraph/0.10.7
  2) GCCcore/12.3.0    7) XZ/5.4.2           12) libevent/2.1.12   17) OpenMPI/4.1.5  22) CMake/3.26.3      27) ScaLAPACK/2.2.0-fb  32) Python/3.11.3    37) Z3/4.12.2
  3) zlib/1.2.13       8) libxml2/2.11.4     13) UCX/1.14.1        18) ncurses/6.4    23) OpenBLAS/0.3.23   28) libreadline/8.2     33) GMP/6.2.1        38) Clang/16.0.6
  4) binutils/2.40     9) libpciaccess/0.17  14) libfabric/1.18.0  19) bzip2/1.0.8    24) FlexiBLAS/3.3.1   29) Tcl/8.6.13          34) GLPK/5.0         39) cffi/1.15.1
  5) GCC/12.3.0       10) hwloc/2.9.1        15) PMIx/4.2.4        20) cURL/8.0.1     25) FFTW/3.3.10       30) SQLite/3.42.0       35) arpack-ng/3.9.0  40) python-igraph/0.11.2

 

(baobab)-[alberta@login2 snapatac2]$ python
Python 3.11.3 (main, Oct  2 2023, 12:57:16) [GCC 12.3.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import snapatac2 as snap
>>> snap.__version__
'2.5.1'

Let me know if it’s working for you

Dear Adrien,

sorry for only asnwering now, I totally overlooked your message.
I did what you suggested and it worked like a charm :slight_smile:

Thank you very very much!!
Anna