Hi,
From your first message it seems like you are running this calculation
on a cluster. Normally they have a time limit for processes ran outside
the queuing system, so my guess is that cpptraj is getting killed after
reaching this time limit. Maybe you could try to split the job in
several parts, making sure that each of them can run within the time
limit. Alternatively, you could use the queueing system to run the full
command.
I hope this helps,
Mariano
On 22/03/2021 18:18, MYRIAN TORRES RICO wrote:
> Hi Dan,
>
> I have ran this calculation directly and effectively it doesn't
> requires very memory...
>
> Thanks in advance,
>
>
> Myriam
> Daniel Roe <daniel.r.roe.gmail.com> escribió:
>
>> Hi,
>>
>> It doesn't look like you're doing anything very memory intensive; 4
>> double precision data sets of length 36842 is like 1 MB worth of data
>> total. What version of cpptraj are you using? Are you running this
>> directly or via a queuing system (e.g. slurm)?
>>
>> -Dan
>>
>> On Mon, Mar 22, 2021 at 5:38 AM MYRIAN TORRES RICO
>> <myriam.torres.iiq.csic.es> wrote:
>>>
>>> Hi alls,
>>>
>>> I have a problem when I launch cpptraj because the calculation stops at 40%:
>>>
>>>
>>> PARAMETER FILES (1 total):
>>> 0: smp-193-ptn3rig.top, 88835 atoms, 28975 res, box: Orthogonal,
>>> 28823 mol, 28811 solvent
>>>
>>> INPUT TRAJECTORIES (1 total):
>>> 0: 'smp-193ptn_vcon3.mdcrd' is an AMBER trajectory, Parm
>>> smp-193-ptn3rig.top (Orthogonal box) (reading 36842 of 36842)
>>> Coordinate processing will occur on 36842 frames.
>>>
>>> BEGIN TRAJECTORY PROCESSING:
>>> .....................................................
>>> ACTION SETUP FOR PARM 'smp-193-ptn3rig.top' (4 actions):
>>> 0: [pucker p1 .2175 .2190 .2187 .2184 .2178 @2177 out pucker1.dat
>>> cremer amplitude theta range360]
>>> [.2175](1) [.2190](1) [.2187](1) [.2184](1) [@2178](1) [@2177](1)
>>> 1: [pucker p2 .2193 .2207 @2205 @2202 @2196 @2195 out pucker2.dat
>>> cremer amplitude theta range360]
>>> [.2193](1) [.2207](1) [@2205](1) [@2202](1) [@2196](1) [@2195](1)
>>> 2: [pucker p3 @2218 @2233 @2230 @2227 @2221 @2220 out pucker3.dat
>>> cremer amplitude theta range360]
>>> [@2218](1) [@2233](1) [@2230](1) [@2227](1) [@2221](1) [@2220](1)
>>> 3: [pucker p4 .2236 .2250 .2248 .2245 @2239 @2238 out pucker4.dat
>>> cremer amplitude theta range360]
>>> [.2236](1) [.2250](1) [.2248](1) [@2245](1) [@2239](1) [@2238](1)
>>> ----- smp-193ptn_vcon3.mdcrd (1-36842, 1) -----
>>> 0% 10% 20% 30% 40% Killed
>>>
>>>
>>>
>>> Any idea? Maybe is the cluster's problem?
>>>
>>> Thanks in advance,
>>>
>>>
>>> Myriam
>>>
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
Dr. Mariano Curti
Postdoctoral researcher - Romero Group
Institute of Chemical Research of Catalonia (ICIQ)
Av. Països Catalans 16 – 43007 Tarragona (Spain)
mcurti.iciq.es
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Mar 23 2021 - 01:30:02 PDT
