Summary: | sci-chemistry/gromacs installs with Genoo Prefix on amd64-linux | ||
---|---|---|---|
Product: | Gentoo/Alt | Reporter: | Reinis Danne <rei4dan> |
Component: | Prefix Support | Assignee: | Justin Lecher (RETIRED) <jlec> |
Status: | RESOLVED FIXED | ||
Severity: | enhancement | CC: | alexxy, junghans, prefix |
Priority: | High | ||
Version: | unspecified | ||
Hardware: | x86 | ||
OS: | Linux | ||
Whiteboard: | |||
Package list: | Runtime testing required: | --- | |
Attachments: |
gromsca-4.0.7.ebuild prefix patch
Patch for the latest ebuild in the tree |
Description
Reinis Danne
2010-01-22 16:31:49 UTC
Created attachment 217183 [details, diff]
gromsca-4.0.7.ebuild prefix patch
I have an issue running gromacs in prefix using lam-mpi: $ lamboot LAM 7.1.4/MPI 2 C++ - Indiana University $ mpirun -np 2 mdrun -s mol_min.tpr -deffnm mol_min & [1] 21409 $ ----------------------------------------------------------------------------- The selected RPI failed to initialize during MPI_INIT. This is a fatal error; I must abort. This occurred on host myhost (n0). The PID of failed process was 21410 (MPI_COMM_WORLD rank: 0) ----------------------------------------------------------------------------- But the mpirun process and associated mdrun processes doesn't die, but they are not doing any work either (0% CPU usage), ang go away only if I terminate one of mdrun processes manually. In serial it runs. Justin (jlec), Care to fix this bug? Can do that, but I am actually not using gromacs until now. I merged the changes into gromacs-4.0.7-r3 in science overlay. @justin: Can you take a look at it, because I am not very familiar with prefix. Looks good so far. Do we have an open bug for the other changes you made? I discussed them with alexxy, basically it is all trivial. I added static-libs use flag and included patches from the stable branch of the upstream repo (the name of the patch is not optimal, we can fix that). So I guess this bug can be closed. Not until it is committed into the prefix tree. The ebuilds in the tree are broken for prefix. As the documentation says DESTDIR for make install should not be changed: http://www.gentoo.org/proj/en/gentoo-alt/prefix/techdocs.xml Created attachment 237999 [details, diff]
Patch for the latest ebuild in the tree
Fixed in science overlay fixed in the portage tree by alexxy, yesterday. |