Hi Jorge, I'm not sure if anyone ever replied to you on this, if not I'm guessing it's because you asked a hard question! In EasyBuild we would not install things using Anaconda, instead we would figure out how to resolve the dependencies using EasyBuild. For this piece of software this is actually not so difficult a task as all the libraries it links to are listed in https://github.com/sharc-md/sharc/blob/master/source/Makefile#L59-L67. sharc-md seems to require libfhdf.so and libdf.so which is actually HDF4, the other libraries would be satisfied by libjpeg-turbo and HDF5. So, if you had the dependencies installed and loaded: https://github.com/easybuilders/easybuild-easyconfigs/blob/develop/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-11.3.0.eb https://github.com/easybuilders/easybuild-easyconfigs/blob/develop/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-2.1.3-GCCcore-11.3.0.eb https://github.com/easybuilders/easybuild-easyconfigs/blob/develop/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-gompi-2022a.eb (which requires HDF5) and you tell the makefile to use OpenBLAS by changing https://github.com/sharc-md/sharc/blob/master/source/Makefile#L93 to LD= -lflexiblas -lfftw3 -lgfortran $(NETCDF_LIB) your application might compile with the Makefile. This is not an EasyBuild recipe, there would still be more work to do to get that, but it might be enough for you to actually *use *sharc-md
Alan On Mon, 8 Aug 2022 at 18:39, Jorge Torres Rodriguez < [email protected]> wrote: > Hello dear easybuild staff, > > My name is Jorge Torres and I am phD student at the FU Berlin in the > physics department. I am trying to install some software in an HPC cluster > which works under the easybuild plattform. I have subscribed to the > mailing list but I am not sure how it works so I send this email to you > and also attach it to the owners to see if I can get some advice. > The software is called SHARC and is a free software that works in linux. > Its repository page is > https://github.com/sharc-md/sharc/blob/master/INSTALL > > Also, I got a message from the administrator from the HPC center, which > says : > > "The instructions to install the program are a bit vague, e.g. > > edit the Makefile by adjusting the > USE_PYSHARC > USE_COMPILER > USE_LIBS > ANACONDA > variables. > > EasyBuild is about automation, but if there is not obvious how to > install the software by hand, it will not be easy to automate. > > The program also uses Anaconda to provide dependencies such as HDF5, but > with EasyBuild such dependencies are usually packaged as separate > modules. This will also make it harder to integrate into EasyBuild. In > fact, I would assume that a separate EasyBlock would be necessary, which > is a part of the EasyBuild framework which encapsulates the specific build > mechanism for a piece of software. Writing such an EasyBlock is not > trivial. It is much better if software uses a standard installation > procedure, since EasyBlock for such standard mechanisms already exist." > > I have installed this program in my computer but since the program run in > parallel with the quantum chemistry software ORCA, the calculations are > very slow. I was wondering if you have received any question on this > software before or on any similar program which needs to be installed by > hand. If yes, is there any instruction for easy configuration? I tried to > install it too but at some point I need to have some administrator > permission to install some program by sudo. This is the main issue I got: > > > error: cannot find -lblas > > > error: cannot find -llapack > > This error I also got on my computer but then I could add the libraries by > sudo apt-get install libblas-dev liblapack-dev > > Then I got an answer of the administrator: > > "No users on the HPC system can run 'sudo' and the 'apt-get' would be > wrong anyway, because the operating system, CentOS, is not Debian-based, > but RedHat-based, and so the package manager is not 'apt' but rather > 'yum'." > > Then there is a makefile whit a command line that needs to be changed from: > > LD= -lblas -llapack -lfftw3 -lgfortran $(NETCDF_LIB) > > to > > LD= -lopenblas -lscalapack -lfftw3 -lgfortran $(NETCDF_LIB) > > since the 'foss' toolchain contains OpenBLAS rather than BLAS and > ScaLAPACK rather than LAPACK. > > Also, the administrator told me that he needs to install the Ancaconda > packages > > hdf5, hdf5_hl, netcdf, mfhdf, df, jpeg, gcc > > Some of these packages are also available via EasyBuild, namely > > - HDF5 > - netCDF > - GCC (included in foss) > > Via conda, the administrator was able to install > > - hdf > - jpeg > > > but he wasn't able to install > > - hdf5_hl > - netcdf > - mfhdf > - df > > via conda. He said that he don't know what channel or channels has/have > to be set for this. Thus, he cannot say whether installing this way will > work. > > For the moment this is my query and I will be very greatful if you can > reply to me if there is any solution. For your attention thank you very > much. > > best > > Jorge Torres > >
