Dear Peter,
in principle this solution is available to everyone and i would love to see that it is also helpful to others. In principle the idea of Nix is to have deterministic environments, that always work on the target as they must be independent from distribution packages/libraries. In the end i hope to be able to get rid of the hazzle of environment modules on our cluster and at the same time have an easy solution to install the software also on a local workstation without teaching the whole group how to compile e.g. OpenMolcas from scratch.
We also have programs like
Pysisyphus
, that wraps QC software to perform tasks and that heavily relies on sane installations of those packages. Nix provides nice tools to integrate all the stuff and simplify wrappers and configuration files for such programs.
If you are interested, i have tried to describe in the
readme of my nix repo
how to use it. So far it seems to work on our Debian, OpenSuse and CentOS systems without trouble.
Using programs like Gaussian, ORCA, MRCC, etc just requires the user to obtain the license and tarballs themselves. Nix is only providing an installer.
Regarding the permission problem, i have some idea what is going on there:
The problem is indeed in this part, starting with the "do" loop in line 8306 of integ.f, where you loop over the atoms in the molecule, i guess.
In this loop for every unique element the density is generated by performing an atomic calculation, which copies the basis of the element to "mrccjunk/" (lines 8526 and 8529-8530), correct?
Now this works fine for the first element in a calculation and without any problems for inputs with just one element. For example, the MINP_3He_cc-pVTZ-RPAX2 test runs fine, as it only has a single element. MINP_Benzene2+_cc-pVDZ_DF-ROHF crashes as it has two elements. C is first in the input and the density for it is just generated without problems. When reaching the hydrogens, MRCC crashes with the error from the last post. Now in "mrccjunk/" there is the following:
Code:
insgesamt 916K
drwxrwxrwx 1 phillip phillip 306 Jul 2 11:50 .
drwxr-xr-x 1 phillip phillip 162 Jul 2 11:50 ..
-rw-rw-rw- 1 phillip phillip 78 Jul 2 11:50 COORD.xyz
-rw-rw-rw- 1 phillip phillip 0 Jul 2 11:50 DAO
-rw-rw-rw- 1 phillip phillip 38 Jul 2 11:50 EXIT
-rw-rw-rw- 1 phillip phillip 1,2K Jul 2 11:50 FOCK
-rw-rw-rw- 1 phillip phillip 240 Jul 2 11:50 fort.11
-rw-rw-rw- 1 phillip phillip 127 Jul 2 11:50 fort.55
-r--r--r-- 1 phillip phillip 331K Jul 2 11:50 GENBAS
-rw-rw-rw- 1 phillip phillip 261 Jul 2 11:50 iface
-rwxrwxrwx 1 phillip phillip 1,6K Jul 2 11:50 junkscript
-rw-rw-rw- 1 phillip phillip 2,2K Jul 2 11:50 KEYWD
-rw-rw-rw- 1 phillip phillip 322 Jul 2 11:50 MINP
-rw-rw-rw- 1 phillip phillip 1,2K Jul 2 11:50 MOCOEF
-rw-rw-rw- 1 phillip phillip 12K Jul 2 11:50 MOLDEN
-rw-rw-rw- 1 phillip phillip 99 Jul 2 11:50 MOLDEN.perm
-rw-rw-rw- 1 phillip phillip 27 Jul 2 11:50 OCCUP
-rw-rw-rw- 1 phillip phillip 672 Jul 2 11:50 OEINT
-rw-rw-rw- 1 phillip phillip 0 Jul 2 11:50 pids
-rw-rw-rw- 1 phillip phillip 336 Jul 2 11:50 PRINT
-rw-rw-rw- 1 phillip phillip 5 Jul 2 11:50 ROUTE
-rw-rw-rw- 1 phillip phillip 608 Jul 2 11:50 SCFDENSITIES
-rw-rw-rw- 1 phillip phillip 272 Jul 2 11:50 SCHOL
-rw-rw-rw- 1 phillip phillip 672 Jul 2 11:50 SROOT
-rw-rw-rw- 1 phillip phillip 240 Jul 2 11:50 SYMTRA
-rw-rw-rw- 1 phillip phillip 2,5K Jul 2 11:50 TEDAT
-rw-rw-rw- 1 phillip phillip 2,4K Jul 2 11:50 TEINT
-rw-rw-rw- 1 phillip phillip 487K Jul 2 11:50 VARS
So "GENBAS" is the only file, which has only read permissions, as they are probably inherited from the original read only permissions of nix-store. Now, when the second loop iterations for H atoms come, "integ" tries to copy "$mrccpath/BASIS/H" to "mrccjunk/GENBAS", which fails as the old "GENBAS" has no write permissions. I have tried to work around this, by applying the sledgehammer and execute
Code:
umask 0000
alias cp="cp --no-preserve=all"'
before invocation of any mrcc executable, but unfortunately this does not work. I guess "ishell" is not picking up the alias.
Regarding the "~/.nix-profile/bin/BASIS" and location of the BASIS directory:
this "~/.nix-profile directory" is actually the place where all nix stuff is being installed. It contains symlinks for the installed programs to the nix-store, where the actual files live.
"~/.nix-profile/bin/" looks like:
Code:
insgesamt 224K
dr-xr-xr-x 1 root root 996 Jan 1 1970 .
dr-xr-xr-x 1 root root 80 Jan 1 1970 ..
lrwxrwxrwx 1 root root 69 Jan 1 1970 BASIS -> /nix/store/8824imlk8gpgxn4nm1d12vqm1f4w3z0w-mrcc-2020.02.22/bin/BASIS
lrwxrwxrwx 1 root root 68 Jan 1 1970 ccsd -> /nix/store/8824imlk8gpgxn4nm1d12vqm1f4w3z0w-mrcc-2020.02.22/bin/ccsd
lrwxrwxrwx 1 root root 72 Jan 1 1970 ccsd_mpi -> /nix/store/8824imlk8gpgxn4nm1d12vqm1f4w3z0w-mrcc-2020.02.22/bin/ccsd_mpi
lrwxrwxrwx 1 root root 67 Jan 1 1970 cis -> /nix/store/8824imlk8gpgxn4nm1d12vqm1f4w3z0w-mrcc-2020.02.22/bin/cis
...
So i guess my last resort would be to copy more or less the entire mrcc installation directory with a wrapper script to the directory from which mrcc was called, set correct permissions on it and call these files then, which can have write permissions for the user. But this is even more extreme. If you see another solution, this would be very nice.
Sorry for the long post and thank you again. Best wishes
Phillip
