Closed pavelToman closed 1 month ago
Hi @pavelToman!
Could you help me please with installing micro-sam from sources by CMake, make, pip install? I can not use conda/mamba for this.
Yes, happy to help! It may take a bit of time, but if you get an easybuild recipe we'd also be interested in having a reference to it :). And in general this should be possible, all dependencies are either installable by CMake or pip.
First of all I can not find which nifty I should install as a dependency, is it this one? https://github.com/DerThorsten/nifty/tree/master
Yes, that is the correct nifty. The other dependency that might be a bit tricky to find / install is vigra: https://github.com/ukoethe/vigra
For now the vigra
and nifty
seems fine. I was able to build them.
But there is a problem with z5py
, could you hint me please?
I am hitting error during make
step:
In file included from /scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/xtensor/0.21.10-foss-2023a/include/xtensor/xstorhpp:23,
from /scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/xtensor/0.21.10-foss-2023a/include/xtensor/xbuffdaptor.hpp:22,
from /scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/xtensor/0.21.10-foss-2023a/include/xtensor-pythoarray.hpp:17,
from /tmp/vsc47063/easybuild/build/z5py/2.0.17/foss-2023a/z5-2.0.17/src/python/lib/z5py.cxx:8:
/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/xtensor/0.21.10-foss-2023a/include/xtensor/xtensor_simd.hpp:65:18: errset_simd has not been declared in xsimd
65 | using xsimd::set_simd;
| ^~~~~~~~
/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/xtensor/0.21.10-foss-2023a/include/xtensor/xtensor_simd.hpp:66:18: errload_simd has not been declared in xsimd
66 | using xsimd::load_simd;
| ^~~~~~~~~
/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/xtensor/0.21.10-foss-2023a/include/xtensor/xtensor_simd.hpp:67:18:or: store_simd has not been declared in xsimd
67 | using xsimd::store_simd;
... and many more same errors about simd
.
I have in dependencies:
I can see there is maybe a problem related to: https://github.com/constantinpape/z5/issues/218
nifty
v1.2.1 has in the environment file:
z5py
v2.0.17 has in the environment file:
and for z5py
v2.0.16:
It seems I can not fullfit both the nifty
and z5py
requirements for xtensor
.
Any idea please, how to solve this?
Can you see if building both nifty
and z5py
with these dependencies works:
z5py
v2.0.17 has in the environment file:* xtensor >=0.24,<0.25 * xtensor-python >=0.26,<0.27 * xsimd >=8,<9
I have a local build of nifty that works in these settings, and I assume that the pin of xtensor
in nifty
is too conservative.
Let me know if this works. If not I will double check my build environment and share it here (but will only have time for this tomorrow.)
Yes it works! I update versions of xtensor
and xtensor-python
and it seems nifty
has no problem with more recent xtensor versions :) Thank you!
@constantinpape thank you for your help! It seems micro-sam can be installed by EasyBuild and is ready to be tested by researchers now.
Thanks @pavelToman! I will also add a link to the recipe in the docs.
Hello micro-sams! I would like to install your micro-sam on HPC for UGent researchers. We are using EasyBuild for handling installations and softwares. Could you help me please with installing micro-sam from sources by CMake, make, pip install? I can not use conda/mamba for this. First of all I can not find which
nifty
I should install as a dependency, is it this one? https://github.com/DerThorsten/nifty/tree/master