Install new python module snapatac2

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1

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

2

Hi @Anna.Ramisch

I am on it :slight_smile:

I keep you in touch !

1 Like
3

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!

4

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

5

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