Search found 16 matches

by bbrydsoe
08 May 2015, 11:33
Forum: Installing Dalton
Topic: Dalton 2015 (OpenMPI, MKL, GCC) fails on more than one node
Replies: 11
Views: 16187

Re: Dalton 2015 (OpenMPI, MKL, GCC) fails on more than one n

No, setting DALTON_LAUNCHER doesn't work. The tests fail in all but a few cases. If I instead do as I described, all tests pass. It looks like it ought to be the same, if you set DALTON_LAUNCHER or make the changes I did, but for some reason it is not. May be due to some weirdness with our batch sys...
by bbrydsoe
04 May 2015, 15:59
Forum: Installing Dalton
Topic: Dalton 2015 (OpenMPI, MKL, GCC) fails on more than one node
Replies: 11
Views: 16187

Re: Dalton 2015 (OpenMPI, MKL, GCC) fails on more than one n

No, it does not mean append to. It was supposed to be -> to mean "change to", so yes replace by what comes after. I don't know why I wrote >> instead.
by bbrydsoe
04 May 2015, 14:32
Forum: Installing Dalton
Topic: Dalton 2015 (OpenMPI, MKL, GCC) fails on more than one node
Replies: 11
Views: 16187

Re: Dalton 2015 (OpenMPI, MKL, GCC) fails on more than one n

After some tests, I found that making these changes in the dalton and lsdalton files worked:

$MPIEXEC -np $optn $DALTON_EXECUTABLE >> srun $DALTON_EXECUTABLE

$MPIEXEC -np $optn $MPI >> srun $MPI


and then run with

dalton -N <procs> -noappend -t <some tempdir> ....

in the job script.
by bbrydsoe
29 Apr 2015, 13:12
Forum: Installing Dalton
Topic: Dalton 2015 (OpenMPI, MKL, GCC) fails on more than one node
Replies: 11
Views: 16187

Re: Dalton 2015 (OpenMPI, MKL, GCC) fails on more than one n

Unfortunately, they way sbcast is set up on our system, the files got copied to the root of /scratch on each node, instead of to the directory that is created for the job. However, it looks like it runs when I do something like this: ../dalton -N 8 -noappend -t `pwd`/tmp dft_b3lyp_nosym.dal H2O_intg...
by bbrydsoe
29 Apr 2015, 11:47
Forum: Installing Dalton
Topic: Dalton 2015 (OpenMPI, MKL, GCC) fails on more than one node
Replies: 11
Views: 16187

Re: Dalton 2015 (OpenMPI, MKL, GCC) fails on more than one n

Yes, I have the value for DALTON_NUM_MPI_PROCS set to 8. Each node has its own /scratch space, so it could definitely be the cause of the error! I am currently just trying to run one of the test-cases, so I created a directory with the files for it in and started it with /home/b/bbrydsoe/pfs/Dalton2...
by bbrydsoe
28 Apr 2015, 16:44
Forum: Installing Dalton
Topic: Dalton 2015 (OpenMPI, MKL, GCC) fails on more than one node
Replies: 11
Views: 16187

Dalton 2015 (OpenMPI, MKL, GCC) fails on more than one node

I have installed Dalton 2015 on a Linux Ubuntu 12.04 system, with GCC 4.6, Openmpi 1.8.1, and MKL 11.2. Configured with ./setup --fc=mpif90 --cc=mpicc --cxx=mpicxx --mpi -D BLAS_TYPE=MKL -D LAPACK_TYPE=MKL build_gcc All tests pass when I run on one node, but now I tested running on more than one nod...
by bbrydsoe
24 Apr 2015, 14:23
Forum: Installing Dalton
Topic: Dalton with OpenMPI, GCC, ACML - testing fails.
Replies: 18
Views: 22026

Re: Dalton with OpenMPI, GCC, ACML - testing fails.

I made some more tests.

I could not get it to compile with Intel and Impi, since it triggered a compiler bug, but I found that using MKL instead of ACML (and then otherwise compiling with GCC 4.6.3 and OpenMPI 1.8.1) works. All tests are passed now :)

Thanks for your help, guys!
by bbrydsoe
23 Apr 2015, 10:36
Forum: Installing Dalton
Topic: Dalton with OpenMPI, GCC, ACML - testing fails.
Replies: 18
Views: 22026

Re: Dalton with OpenMPI, GCC, ACML - testing fails.

I don't know about srun but "make test" uses the dalton script which in turn executes mpirun when DALTON_NUM_MPI_PROCS is larger than one. Therefore it makes sense that "mpirun make test" doesn't work. I could suspect something similar with srun although I don't know how that works. That does expla...
by bbrydsoe
23 Apr 2015, 10:32
Forum: Installing Dalton
Topic: Dalton with OpenMPI, GCC, ACML - testing fails.
Replies: 18
Views: 22026

Re: Dalton with OpenMPI, GCC, ACML - testing fails.

So if I just set DALTON_NUM_MPI_PROCS then that should be enough?
by bbrydsoe
22 Apr 2015, 14:06
Forum: Installing Dalton
Topic: Dalton with OpenMPI, GCC, ACML - testing fails.
Replies: 18
Views: 22026

Re: Dalton with OpenMPI, GCC, ACML - testing fails.

Good idea checking what happened on the node! It looks like it is actually running on 8 cores (possibly because I set export DALTON_NUM_MPI_PROCS=8 in my submit script). I didn't think it would when I didn't use srun or mpirun. I will try do a run with -noappend flag set and see what happens. I am c...
by bbrydsoe
22 Apr 2015, 13:31
Forum: Installing Dalton
Topic: Dalton with OpenMPI, GCC, ACML - testing fails.
Replies: 18
Views: 22026

Re: Dalton with OpenMPI, GCC, ACML - testing fails.

I tried compiling without any optimizations. No change. After some more tests I found that it would seem the problem has something to do with running certain of the tests on more than one core. The tests that failed only do so when I do mpirun -np <cores> make test or srun make test (with more than ...
by bbrydsoe
20 Apr 2015, 15:56
Forum: Installing Dalton
Topic: Dalton with OpenMPI, GCC, ACML - testing fails.
Replies: 18
Views: 22026

Re: Dalton with OpenMPI, GCC, ACML - testing fails.

One question: you are running with the scratch directory DALTON_TMPDIR set to /scratch. I can readily imagine that /scratch is your scratch filesystem, but on most platforms it is more common to have directories like /scratch/taylor underneath which particular runs set up their scratch directories ...
by bbrydsoe
20 Apr 2015, 14:38
Forum: Installing Dalton
Topic: Dalton with OpenMPI, GCC, ACML - testing fails.
Replies: 18
Views: 22026

Re: Dalton with OpenMPI, GCC, ACML - testing fails.

I am unsure where the logs for the failed tests are? All I can find in test/ are the succeeded tests. There are also files of the type "test_walk_vibave2_failed_2015-04-17T15_41-21885", but they appear to be binary files? There is a little bit of info in the main "LastTest.log" (too big to attach),...
by bbrydsoe
20 Apr 2015, 14:09
Forum: Installing Dalton
Topic: Dalton with OpenMPI, GCC, ACML - testing fails.
Replies: 18
Views: 22026

Re: Dalton with OpenMPI, GCC, ACML - testing fails.

dear Birgitte, we do not have an official recommended set of compilers and libraries. however, i will point you to this site that can be useful: https://testboard.org/cdash/index.php?project=Dalton here we aggregate nightly test results from a number of machines and compilers/libaries. scroll to th...
by bbrydsoe
20 Apr 2015, 14:05
Forum: Installing Dalton
Topic: Dalton with OpenMPI, GCC, ACML - testing fails.
Replies: 18
Views: 22026

Re: Dalton with OpenMPI, GCC, ACML - testing fails.

Although you supplied a list of the failed tests, you do not appear to have posted any actual error messages as to why the tests failed? Do the tests run apparently to completion but then give an error because the final result(s) are incorrect? Or do the test jobs die at some point (or perhaps do n...
by bbrydsoe
20 Apr 2015, 11:33
Forum: Installing Dalton
Topic: Dalton with OpenMPI, GCC, ACML - testing fails.
Replies: 18
Views: 22026

Dalton with OpenMPI, GCC, ACML - testing fails.

I have compiled Dalton 2015 with OpenMPI 1.6.5, GCC 4.6.3, and ACML 5.3.1. OS is Linux Ubuntu 12.04. I configure with export MATH_ROOT='/lap/acml/5.3.1/gfortran64_fma4' ./setup --fc=mpif90 --cc=mpicc --cxx=mpicxx --mpi -D BLAS_TYPE=ACML -D LAPACK_TYPE=ACML build_gcc_noscalapack_acml_32 It then compi...