[gmx-users] Force fields

2018-04-27 Thread Alex 
Dear all,
I have the Gromos-54A7 force fields (FF) for the molecule number 1 in the
below link, using thoes how I can have the FF for the molecules number 2,3
and 4 in the same link without doing extra calculations? What could be the
relation between the FF of other molecule with the FF of molecule number 1?
Molecules 2,3 and 4 are the output of a kind of condensation reaction
happening between two number 1 molecule in sequence.

https://drive.google.com/open?id=1zqLSSdtDHrdVMO567WFSavAiVN-knLuX

Thank you.
Regards,
Alex
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Re: [gmx-users] strange GPU load distribution

2018-04-27 Thread Alex 

I see. :) I will check again when I am back at work.

Thanks!

Alex


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  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  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   = 50; 1 ns
nstcomm  = 100
; Output control
nstxout  = 5
nstvout  = 5
nstfout  = 0
nstlog   = 5
nstenergy= 5
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  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  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  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

Re: [gmx-users] strange GPU load distribution

2018-04-27 Thread Mark Abraham 
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  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  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   = 50; 1 ns
> >> nstcomm  = 100
> >> ; Output control
> >> nstxout  = 5
> >> nstvout  = 5
> >> nstfout  = 0
> >> nstlog   = 5
> >> nstenergy= 5
> >> 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  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  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  wrote:
> >>
> >>> Hi all,
> >>>
> >>> I am running GMX 2018 with gmx mdrun -pinoffset 0 -pin on -nt 24
> > -ntmpi 4
> >>> -npme 1 -pme

Re: [gmx-users] strange GPU load distribution

2018-04-27 Thread Alex 
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  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   = 50; 1 ns
nstcomm  = 100
; Output control
nstxout  = 5
nstvout  = 5
nstfout  = 0
nstlog   = 5
nstenergy= 5
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  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  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  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

Re: [gmx-users] strange GPU load distribution

2018-04-27 Thread Mark Abraham 
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  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   = 50; 1 ns
> nstcomm  = 100
> ; Output control
> nstxout  = 5
> nstvout  = 5
> nstfout  = 0
> nstlog   = 5
> nstenergy= 5
> 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  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  >
> > 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  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  >
> >> > 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  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 |
> >> > >

Re: [gmx-users] strange GPU load distribution

2018-04-27 Thread Alex 
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   = 50; 1 ns
nstcomm  = 100
; Output control
nstxout  = 5
nstvout  = 5
nstfout  = 0
nstlog   = 5
nstenergy= 5
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  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 
> 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  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 
>> > 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  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

Re: [gmx-users] strange GPU load distribution

2018-04-27 Thread Alex 
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 
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  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 
> > 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  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
> > > >
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> > > > 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
> > >
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> > > Support/Mailing_Lists/GMX-Users_List before posting!
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Re: [gmx-users] Box size to be considered in editconf

2018-04-27 Thread Justin Lemkul 



On 4/27/18 1:36 PM, SHYANTANI MAITI wrote:

Dear all,
What should be the size of a cubic box in the command editconf for
simulating a protein-protein complex consisting of 500 residues altogether?


Depends entirely upon the geometry of the protein itself. The box size 
for a globular protein will be totally different from an elongated one. 
Use the -d flag to set a suitable buffer size and let editconf work its 
magic.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

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Re: [gmx-users] strange GPU load distribution

2018-04-27 Thread Mark Abraham 
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  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 
> 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  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.
> > --
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> >
> > * Please search the archive at http://www.gromacs.org/
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Re: [gmx-users] strange GPU load distribution

2018-04-27 Thread Alex 
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 
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  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
> >
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> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-requ...@gromacs.org.
> --
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>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
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[gmx-users] Box size to be considered in editconf

2018-04-27 Thread SHYANTANI MAITI 
Dear all,
What should be the size of a cubic box in the command editconf for
simulating a protein-protein complex consisting of 500 residues altogether?
 Thanks in advance.

-- 
Best regards,
*Shyantani Maiti*
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Re: [gmx-users] strange GPU load distribution

2018-04-27 Thread Szilárd Páll 
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  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!
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