hi again,
3 answers are hidden somewhere below ..
Am 28.10.2015 um 15:45 schrieb Mark Abraham:
Hi,
On Wed, Oct 28, 2015 at 3:19 PM Vedat Durmaz <dur...@zib.de> wrote:
Am 27.10.2015 um 23:57 schrieb Mark Abraham:
Hi,
On Tue, Oct 27, 2015 at 11:39 PM Vedat Durmaz <dur...@zib.de> wrote:
hi mark,
many thanks. but can you be a little more precise? the author's only
hint regarding mpi is on this site
"http://rashmikumari.github.io/g_mmpbsa/How-to-Run.html"; and related to
APBS. g_mmpbsa itself doesn't understand openmp/mpi afaik.
the error i'm observing is occurring pretty much before apbs is started.
to be honest, i can't see any link to my initial question ...
It has the sentence "Although g_mmpbsa does not support mpirun..." aprun
is
a form of mpirun, so I assumed you knew that what you were trying was
actually something that could work, which would therefore have to be with
the APBS back end. The point of what it says there is that you don't run
g_mmpbsa with aprun, you tell it how to run APBS with aprun. This just
avoids the problem entirely because your redirected/interactive input
goes
to a single g_mmpbsa as normal, which then launches APBS with MPI
support.
Tool authors need to actively write code to be useful with MPI, so unless
you know what you are doing is supposed to work with MPI because they say
it works, don't try.
Mark
you are right. it's apbs which ought to run in parallel mode. of course,
i can set the variable 'export APBS="mpirun -np 8 apbs"' [or set 'export
OMP_NUM_THREADS=8'] if i want to split a 24 cores-node to let's say 3
independent g_mmpbsa processes. the problem is that i must start
g_mmpbsa itself with aprun (in the script run_mmpbsa.sh).
No. Your job runs a shell script on your compute node. It can do anything
it likes, but it would make sense to run something in parallel at some
point. You need to build a g_mmpbsa that you can just run in a shell script
that echoes in the input (try that on its own first). Then you use the
above approach so that the single process that is g_mmpbsa does the call to
aprun (which is the cray mpirun) to run APBS in MPI mode.
It is likely that even if you run g_mmpbsa with aprun and solve the input
issue somewhow, the MPI runtime will refuse to start the child APBS with
aprun, because nesting is typically unsupported (and your current command
lines haven't given it enough information to do a good job even if it is
supported).
yes, i've encountered issues with nested aprun calls. so this will
hardly work i guess.
i absolutely
cannot see any other way of running apbs when using it out of g_mmpbs.
hence, i need to run
aprun -n 3 -N 3 -cc 0-7:8-15:16-23 ../run_mmpbsa.sh
This likely starts three copies of g_mmpbsa each of which expect terminal
input, which maybe you can teach aprun to manage, but then each g_mmpbsa
will then do its own APBS and this is completely not what you want.
hmm, to be honest, i would say this is exactly what i'm trying to
achieve. isn't it? i want 3 independent g_mmpbsa runs each of which
executed in another directory with its own APBS. by the way, all
together i have 1800 such directories each containing another trajectory.
if someone is ever (within the next 20 hours!) able to figure out a
solution for this purpose, i would be absolutely pleased.
and of course i'm aware about having given 8 cores to g_mmpbsa, hoping
that it is able to read my input and to run apbs which hopefully uses
all of the 8 cores. the user input (choosing protein, then ligand),
however, "Cannot [be] read". this issue occurs quite early during the
g_mmpbsa process and therefore has nothing to do with the apbs (either
with openmp or mpi) functionality which is launched later.
if i simulate the whole story (spreading 24 cores of a node over 3
processes) using a bash script (instead of g_mmpbsa) which just expects
(and prints) the two inputs during runtime and which i start three times
on one node, everything works fine. i'm just asking myself whether
someone knows why gromacs fails under the same conditions and whether it
is possible to remedy that problem.
By the way, GROMACS isn't failing. You're using a separately provided
program, so you should really be talking to its authors for help. ;-)
mpirun -np 3 gmx_mpi make_ndx
would work fine (though not usefully), if you use the mechanisms provided
by mpirun to control how the redirection to the stdin of the child
processes should work. But handling that redirection is an issue between
you and the docs of your mpirun :-)
Mark
unfortunately, there is only very few information about stdin
redirection associated with aprun. what i've done now is modifying
g_mmpbsa such that no user input is required. starting
aprun -n 3 -N 3 -cc 0-7:8-15:16-23 ../run_mmpbsa.sh
where, using the $ALPS_APP_PE variable, i successfully enter three
directories (dir_1, dir_2, dir_3, all containing identical file names)
and start g_mmpbsa in each of them. now what happens is that all the new
files are generated in the first of the 3 folders (while the two others
are not affected at all). and all new files are generated 3 times (file,
#file1#, #file2#) in a manner which is typical for gromacs' backup
philosophy. so on some (hardware?) level the data of the 3 processes are
not well separated. the supervisors of our HPC system were not able to
figure out the reasons so far. that's why i'm trying to find help here
from someone that was successful in sharing computing nodes in a similar
way.
anyways. thanks for your time so far.
Am 27.10.2015 um 22:43 schrieb Mark Abraham:
Hi,
I think if you check out how the g_mmpbsa author intends you to use MPI
with the tool, your problem goes away.
http://rashmikumari.github.io/g_mmpbsa/Usage.html
Mark
On Tue, Oct 27, 2015 at 10:10 PM Vedat Durmaz <dur...@zib.de> wrote:
hi guys,
I'm struggling with the use of diverse gromacs commands on a Cray XC30
system. actually, it's about the external tool g_mmpbsa which requires
user action during runtime. i get similar errors with other Gromacs
tools, e.g., make_ndx, though, i know that it doesn't make sense to
use
more than one core for make_ndx. however, g_mmpsa (or rather apbs used
by g_mmpbsa) is supposed to be capable of multiple cores using openmp.
so, as long as i assign all of the 24 cores of a computing node to one
process through
aprun -n 1 ../run_mmpbsa.sh
everthing works fine. user input is accepted either interactively, by
using the echo command, or through a here construction (""... << EOF
...
EOF). however, as soon as I try to split the 24 cores of a node to
multiple processes (more than one) using for instance
aprun -n 3 -N 3 -cc 0-7:8-15:16-23 ../run_mmpbsa.sh
(and OMP_NUM_THREADS=8), there is neither an occasion to feed with
user
input in the interactive mode nor it is recognized through echo/here
in
the script. instead, i get the error
>> Source code file: .../gromacs-4.6.7/src/gmxlib/index.c, line:
1192
>> Fatal error:
>> Cannot read from input
where, according to the source code, "scanf" malfunctions. when i use,
for comparison purposes, make_ndx that i would like to feed with "q" i
observe a similar error:
>>Source code file: .../gromacs-4.6.7/src/tools/gmx_make_ndx.c,
line:
1219
>>Fatal error:
>>Error reading user input
here, it's "fgets" which is malfunctioning.
does anyone have an idea what this could be caused by? what do i need
to
consider/change in order to be able to start more than process on one
computing node?
thanks in advance
vedat
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