Why is my bin folder empty?

[Nicola Spallanzani]

Dear Salma,
unfortunately you have to start from scratch. Even if you installed the missing lib you also have to delete and re-install the hdf5 library. Usually should be enough to run "make distclean", but my suggestion is to delete the directory of yambo, download the newer version and try again following these steps:

Code: Select all

apt-get -yqq update
apt-get install build-essential ca-certificates curl file \
       make gcc g++ gfortran git gnupg2 iproute2 \
       unzip m4 wget git zlib1g-dev ssh \
       libmkl-avx libmkl-avx2 libmkl-avx512 libmkl-core libmkl-def \
       libmkl-dev libmkl-gf-ilp64 libmkl-gf-lp64 libmkl-gnu-thread
wget https://github.com/yambo-code/yambo/archive/5.1.1.tar.gz -O yambo-5.1.1.tar.gz 
tar zxfv yambo-5.1.1.tar.gz && cd yambo-5.1.1
./configure --enable-mpi --enable-open-mp \
  --enable-slepc-linalg --disable-hdf5-par-io \
  --enable-msgs-comps --enable-time-profile --enable-memory-profile \
  --with-blas-libs="-L${MKLROOT}/lib/intel64 -Wl,--no-as-needed -lmkl_gf_lp64 -lmkl_gnu_thread -lmkl_core -lgomp -lpthread -lm -ldl" \
  --with-lapack-libs="-L${MKLROOT}/lib/intel64 -Wl,--no-as-needed -lmkl_gf_lp64 -lmkl_gnu_thread -lmkl_core -lgomp -lpthread -lm -ldl" 
make -j4 core
make -j4 all

Best regards,
Nicola

[Peace]

Dear Nicola,
When I used the first command nothing was generated in the terminal. And when I used the second command (I added sudo to it)

Code: Select all

sudo apt-get install build-essential ca-certificates curl file \
       make gcc g++ gfortran git gnupg2 iproute2 \
       unzip m4 wget git zlib1g-dev ssh \
       libmkl-avx libmkl-avx2 libmkl-avx512 libmkl-core libmkl-def \
       libmkl-dev libmkl-gf-ilp64 libmkl-gf-lp64 libmkl-gnu-thread

I got the following message in terminal:

Code: Select all

Intel Math Kernel Library (Intel MKL) ├─────────────────┐
 │                                                                           │ 
 │ Intel MKL's Single Dynamic Library (SDL) is installed on your machine.      
 │ This shared object can be used as an alternative to both libblas.so.3       
 │ and liblapack.so.3, so that packages built against BLAS/LAPACK can          
 │ directly use MKL without rebuild.                                           
 │                                                                             
 │ However, MKL is non-free software, and in particular its source code is     
 │ not publicly available. By using MKL as the default BLAS/LAPACK             
 │ implementation, you might be violating the licensing terms of copyleft      
 │ software that would become dynamically linked against it. Please verify     
 │ that the licensing terms of the program(s) that you intend to use with      
 │ MKL are compatible with the MKL licensing terms. For the case of            
 │ software under the GNU General Public License, you may want to read this    
 │ FAQ:                                                                        
 │                                                                             
 │                                                                             
 │                                  <Ok>                                       
 │                                                      

What should I do regarding that, please?

[Nicola Spallanzani]

Dear Salma,
I'm not sure, but I think you can proceed.
But if you prefer a safe solution, you can install "libopenblas-dev" from apt instead of MKL packages.
In that case the configure line change like this:

Code: Select all

./configure --enable-mpi --enable-open-mp \
  --enable-slepc-linalg --disable-hdf5-par-io \
  --enable-msgs-comps --enable-time-profile --enable-memory-profile \
  --with-blas-libs="-lopenblas" \
  --with-lapack-libs="-lopenblas" 

Otherwise you can install the Intel oneAPI HPC toolkit, that is the optimum solution for Intel architectures:
https://www.intel.com/content/www/us/en ... tools.html
https://www.intel.com/content/www/us/en ... rview.html

Best regards,
Nicola

[Peace]

Dear Nicola,

Thank you so much, following your instructions I fixed the problem

That's what I found in my bin:

Code: Select all

 a2y  c2y  p2y  yambo yambo_nl  yambo_ph  yambo_rt  yambo_sc  ypp ypp_nl  ypp_ph  ypp_rt  ypp_sc 

[Nicola Spallanzani]

Dear Salma,
happy to have been helpful.

Best,
Nicola