Adding instructions for conda environments.

Author: mikibonacci

conda_env/README.md

@@ -0,0 +1,71 @@
+# How to compile Quantum ESPRESSO and Yambo in a conda environment
+
+The following are instructions on how to prepare a conda env (python virtual environment) to then compile Quantum ESPRESSO and Yambo, 
+and run parallel calculations.
+
+```shell
+conda create -n codes python=3.11
+conda activate codes
+```
+
+Once activated the environment, you can proceed with the following sections. 
+Each time you run a calculation, you need the environment to be activated, to have the correct modules...
+
+
+## Prepare a working openmpi env:
+
+```shell
+conda install openmpi hdf5=*=*openmpi*  fftw=*=*openmpi* libxc=*=*cpu* libnetcdf=*=*openmpi* netcdf-fortran=*=*openmpi* libblas lapack scalapack gfortran
+
+conda install -c conda-forge ucx # to have correct MPI communication setup and run in parallel.
+```
+
+OR conda install yambo, to directly download the executables from the conda-forge... but I prefer to compile it by hands (see below sections).
+
+## How to install Quantum ESPRESSO
+
+Download the Quantum ESPRESSO source from gitlab
+
+```shell
+./install/configure --with-hdf5 --enable-openmp 
+```
+
+## How to install Yambo 
+
+A comment on the configure: conda install the dynamic netcdf lib (you know it noticing that in the lib, it is *.so and not *.a, the latter being the static version. Yambo by default does not find the dynamical one, you have to explicitely tell him. like in the line below.)
+
+```shell
+export PATH_YAMBO_LIB="/home/jovyan/.conda/envs/codes/" # the path to your venv: check it via "conda env list"
+
+./configure --enable-mpi --enable-open-mp --with-fft-path=$PATH_YAMBO_LIB --with-hdf5-path=$PATH_YAMBO_LIB --with-netcdf-libs=$PATH_YAMBO_LIB/lib/libnetcdf.so --with-netcdff-libs=$PATH_YAMBO_LIB/lib/libnetcdff.so --disable-hdf5-par-io --with-libxc-path=$PATH_YAMBO_LIB --with-scalapack-libs=$PATH_YAMBO_LIB/lib/libscalapack.so --with-blacs-libs=$PATH_YAMBO_LIB/lib/libscalapack.so --enable-par-linalg
+```
+
+### Special instructions on how to run:
+
+Follow this, if you have trouble in running in parallel:
+
+```shell
+mpirun --mca btl_vader_single_copy_mechanism none  -np 2 /home/jovyan/codes/q-e-kcw/bin/pw.x < Si.scf.in > prova.out
+```
+
+## because:
+
+```shell
+^C^C(codes) jovyan@6f222c4867e7:~/work/koopmans_calcs/interface_yambo/trial_Si/BANDS/KI_uniq$ mpirun --mca btl_vader_single_copy_mechanism 0 -np 2 /home/jovyan/codes/q-e-kcw/bin/pw.x < Si.scf.in > prova.out
+--------------------------------------------------------------------------
+An invalid value was supplied for an enum variable.
+
+  Variable     : btl_vader_single_copy_mechanism
+  Value        : 0
+  Valid values : 1:"cma", 4:"emulated", 3:"none"
+--------------------------------------------------------------------------
+--------------------------------------------------------------------------
+WARNING: Linux kernel CMA support was requested via the
+btl_vader_single_copy_mechanism MCA variable, but CMA support is
+not available due to restrictive ptrace settings.
+
+The vader shared memory BTL will fall back on another single-copy
+mechanism if one is available. This may result in lower performance.
+
+  Local host: 6f222c4867e7
+```