Hi Mark,
We checked and one example is below.
Thanks,
Alex
PID TTY STAT TIME COMMAND
60432 pts/8 Dl+ 0:01 gmx mdrun -table ../../../tab_it.xvg -nt 1 -nb
cpu -pme cpu -deffnm em_steep
On 4/27/2018 2:16 PM, Mark Abraham wrote:
Hi,
What you think was run isn't nearly as useful when troubleshooting as
asking the kernel what is actually running.
Mark
On Fri, Apr 27, 2018, 21:59 Alex <nedoma...@gmail.com> wrote:
Mark, I copied the exact command line from the script, right above the
mdp file. It is literally how the script calls mdrun in this case:
gmx mdrun -nt 2 -nb cpu -pme cpu -deffnm
On 4/27/2018 1:52 PM, Mark Abraham wrote:
Group cutoff scheme can never run on a gpu, so none of that should
matter.
Use ps and find out what the command lines were.
Mark
On Fri, Apr 27, 2018, 21:37 Alex <nedoma...@gmail.com> wrote:
Update: we're basically removing commands one by one from the script
that
submits the jobs causing the issue. The culprit is both EM and the MD
run:
and GPUs are being affected _before_ MD starts loading the CPU, i.e.
this
is the initial setting up of the EM run -- CPU load is near zero,
nvidia-smi reports the mess. I wonder if this is in any way related to
that
timing test we were failing a while back.
mdrun call and mdp below, though I suspect they have nothing to do with
what is happening. Any help will be very highly appreciated.
Alex
***
gmx mdrun -nt 2 -nb cpu -pme cpu -deffnm
mdp:
; Run control
integrator = md-vv ; Velocity Verlet
tinit = 0
dt = 0.002
nsteps = 500000 ; 1 ns
nstcomm = 100
; Output control
nstxout = 50000
nstvout = 50000
nstfout = 0
nstlog = 50000
nstenergy = 50000
nstxout-compressed = 0
; Neighborsearching and short-range nonbonded interactions
cutoff-scheme = group
nstlist = 10
ns_type = grid
pbc = xyz
rlist = 1.4
; Electrostatics
coulombtype = cutoff
rcoulomb = 1.4
; van der Waals
vdwtype = user
vdw-modifier = none
rvdw = 1.4
; Apply long range dispersion corrections for Energy and Pressure
DispCorr = EnerPres
; Spacing for the PME/PPPM FFT grid
fourierspacing = 0.12
; EWALD/PME/PPPM parameters
pme_order = 6
ewald_rtol = 1e-06
epsilon_surface = 0
; Temperature coupling
Tcoupl = nose-hoover
tc_grps = system
tau_t = 1.0
ref_t = some_temperature
; Pressure coupling is off for NVT
Pcoupl = No
tau_p = 0.5
compressibility = 4.5e-05
ref_p = 1.0
; options for bonds
constraints = all-bonds
constraint_algorithm = lincs
On Fri, Apr 27, 2018 at 1:14 PM, Alex <nedoma...@gmail.com> wrote:
As I said, only two users, and nvidia-smi shows the process name. We're
investigating and it does appear that it is EM that uses cutoff
electrostatics and as a result the user did not bother with -pme cpu in
the
mdrun call. What would be the correct way to enforce cpu-only mdrun
when
coulombtype = cutoff?
Thanks,
Alex
On Fri, Apr 27, 2018 at 12:45 PM, Mark Abraham <
mark.j.abra...@gmail.com
wrote:
No.
Look at the processes that are running, e.g. with top or ps. Either
old
simulations or another user is running.
Mark
On Fri, Apr 27, 2018, 20:33 Alex <nedoma...@gmail.com> wrote:
Strange. There are only two people using this machine, myself being
one
of
them, and the other person specifically forces -nb cpu -pme cpu in
his
calls to mdrun. Are any other GMX utilities (e.g. insert-molecules,
grompp,
or energy) trying to use GPUs?
Thanks,
Alex
On Fri, Apr 27, 2018 at 5:33 AM, Szilárd Páll <
pall.szil...@gmail.com
wrote:
The second column is PIDs so there is a whole lot more going on
there
than
just a single simulation, single rank using two GPUs. That would be
one
PID
and two entries for the two GPUs. Are you sure you're not running
other
processes?
--
Szilárd
On Thu, Apr 26, 2018 at 5:52 AM, Alex <nedoma...@gmail.com> wrote:
Hi all,
I am running GMX 2018 with gmx mdrun -pinoffset 0 -pin on -nt 24
-ntmpi 4
-npme 1 -pme gpu -nb gpu -gputasks 1122
Once in a while the simulation slows down and nvidia-smi reports
something
like this:
| 1 12981 C gmx
175MiB |
| 2 12981 C gmx
217MiB |
| 2 13083 C gmx
161MiB |
| 2 13086 C gmx
159MiB |
| 2 13089 C gmx
139MiB |
| 2 13093 C gmx
163MiB |
| 2 13096 C gmx
11MiB |
| 2 13099 C gmx
8MiB |
| 2 13102 C gmx
8MiB |
| 2 13106 C gmx
8MiB |
| 2 13109 C gmx
8MiB |
| 2 13112 C gmx
8MiB |
| 2 13115 C gmx
8MiB |
| 2 13119 C gmx
8MiB |
| 2 13122 C gmx
8MiB |
| 2 13125 C gmx
8MiB |
| 2 13128 C gmx
8MiB |
| 2 13131 C gmx
8MiB |
| 2 13134 C gmx
8MiB |
| 2 13138 C gmx
8MiB |
| 2 13141 C gmx
8MiB |
+-----------------------------------------------------------
------------------+
Then goes back to the expected load. Is this normal?
Thanks,
Alex
--
Gromacs Users mailing list
* Please search the archive at http://www.gromacs.org/Support
/Mailing_Lists/GMX-Users_List before posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
or
send a mail to gmx-users-requ...@gromacs.org.
--
Gromacs Users mailing list
* Please search the archive at http://www.gromacs.org/
Support/Mailing_Lists/GMX-Users_List before posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
or
send a mail to gmx-users-requ...@gromacs.org.
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
or
send a mail to gmx-users-requ...@gromacs.org.
--
Gromacs Users mailing list
* Please search the archive at http://www.gromacs.org/Support
/Mailing_Lists/GMX-Users_List before posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
send a mail to gmx-users-requ...@gromacs.org.
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
send a mail to gmx-users-requ...@gromacs.org.
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
send a mail to gmx-users-requ...@gromacs.org.
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a
mail to gmx-users-requ...@gromacs.org.
