Mpirun There Are Not Enough Slots Available In The System
Describe how Open MPI was installed (e.g., from a source/distribution tarball, from a git clone, from an operating system distribution package, etc.) It was installed from source/distribution tarball. Please describe the system on which you are running. Distributor ID: CentOS Description: CentOS Linux release 7.6.1810 (Core) Release: 7.6.1810. R3.4 + OpenMPI 3.0.0 + Rmpi inside macOS – little bit of mess;) As usual, there are no easy solutions when it comes to R and mac;) First of all, I suggest to get clean, isolated copy of OpenMPI so you can be sure that your installation has no issues with mixed libs. To launch an MPI program, use the mpirun command: mpirun -np 4 ring -t 10000 -s 16 The mpirun command provides the -np flag to specify the number of processes. The value of this parameter should not exceed the number of available physical cores you alloated via qsub. Otherwise, the program will run, but very slowly, as it is multiplexing resources. There are not enough slots available in the system to satisfy the 20 slots that were requested by the application: hostname Either request fewer slots for your application, or make more slots available for use.
I'm trying to use multiple walker metadynamics to simulate the free energy surface of a DNA-protein system.
I installed plumed 2.3.2 with gromacs 2016.3. I'm using just 2 walkers for now but when I use the command:
mpirun -x PATH -x LD_LIBRARY_PATH -x MPI_HOME gmx_mpi mdrun -ntomp 4 -deffnm md -v -dlb yes -pin on -nb gpu -dd 0 0 0 -maxh -1 -plumed plumed.dat -multi 2
I have the following error:
'A requested component was not found, or was unable to be opened. This
means that this component is either not installed or is unable to be
used on your system (e.g., sometimes this means that shared libraries
that the component requires are unable to be found/loaded). Note that
Open MPI stopped checking at the first component that it did not find.
Host: compute-1-3.local
Framework: ess
Component: pmi
--------------------------------------------------------------------------
[compute-1-3.local:24323] [[INVALID],INVALID] ORTE_ERROR_LOG: Error in file runtime/orte_init.c at line 116
--------------------------------------------------------------------------
It looks like orte_init failed for some reason; your parallel process is
likely to abort. There are many reasons that a parallel process can
fail during orte_init; some of which are due to configuration or
environment problems. This failure appears to be an internal failure;
here's some additional information (which may only be relevant to an
Open MPI developer):
orte_ess_base_open failed
--> Returned value Error (-1) instead of ORTE_SUCCESS
--------------------------------------------------------------------------
--------------------------------------------------------------------------
It looks like MPI_INIT failed for some reason; your parallel process is
likely to abort. There are many reasons that a parallel process can
fail during MPI_INIT; some of which are due to configuration or environment
problems. This failure appears to be an internal failure; here's some
additional information (which may only be relevant to an Open MPI
developer):
ompi_mpi_init: orte_init failed
--> Returned 'Error' (-1) instead of 'Success' (0)
--------------------------------------------------------------------------
[compute-1-3.local:24323] *** An error occurred in MPI_Init_thread
[compute-1-3.local:24323] *** on a NULL communicator
[compute-1-3.local:24323] *** Unknown error
[compute-1-3.local:24323] *** MPI_ERRORS_ARE_FATAL: your MPI job will now abort
--------------------------------------------------------------------------
An MPI process is aborting at a time when it cannot guarantee that all
of its peer processes in the job will be killed properly.'
I tried to change the number of ranks by using -np after mpirun but it doesn't work anyway.
Any suggestion about how to solve this problem?
Are Gromacs 2016.3 and plumed 2.3.2 compatible or should I install other versions that work better for the multiple walkers?
NB I'm using Openmpi 2.1.0.
Thank you for your help!
Stefania
From: Alexander Tzanov (Alexander.Tzanov_at_csi.cuny.edu)
Date: Wed Jun 24 2015 - 13:37:01 CDT
- Next message:Baker D.J.: 'NAMD 2.10 on IBM POWER(8) machines'
- Previous message:Axel Kohlmeyer: 'Re: Re: run on sungle node'
- In reply to:Josh Vermaas: 'Re: Re: run on sungle node'
- Next in thread:Axel Kohlmeyer: 'Re: Re: run on sungle node'
- Messages sorted by:[ date ][ thread ][ subject ][ author ][ attachment ]
HI Josh
Thanks for reply. I did not use charmrun in my scripts. However I downloaded and recompiled the newest version (06-2015) from your site with the same options as
before. Now the problem seems to me disapper and NAMD works fine on single node.
#!/bin/bash
#PBS -q production
#PBS -N apoa_job_nsf
#PBS -l select=1:ncpus=4:ngpus=2:mpiprocs=4
#PBS -l place=free
#PBS -V
cd $PBS_O_WORKDIR
NN=`cat $PBS_NODEFILE wc -l`
echo 'Processors received = '$NN >> myout
MM=`cat $PBS_NODEFILE`
echo 'MM = '$MM >> myout
# Use 'mpirun' and point to the MPI parallel executable to run echo '>>>> Begin NAMD MPI Parallel Run ...'
mpirun -np 4 -machinefile $PBS_NODEFILE namd2 +idlepoll +devices 0,1 ./apoa1.namd > apoa1.out
Thanks. $PBS_NODEFILE reports correctly now:
Processors received = 4
MM = compute-0-21.ib compute-0-21.ib compute-0-21.ib compute-0-21.ib
Alex
On Jun 24, 2015, at 12:14 PM, Josh Vermaas <vermaas2_at_illinois.edu<mailto:vermaas2_at_illinois.edu>> wrote:
What does your submit script look like? The error message looks like one from mpirun, not NAMD, so there may be something obvious going on if we were to see what options were given.
-Josh Vermaas
On 6/24/15 11:03 AM, Alexander Tzanov wrote:
Just to clarify a bit more:
NAMD cannot use more than one core on a node. If I run with one core per node,
the NAMD runs. If I ask for more than one core i.e. 4 cores, I got the error:
--------------------------------------------------------------------------------------------------------------------------
There are not enough slots available in the system to satisfy the 4 slots
that were requested by the application:
namd2
Either request fewer slots for your application, or make more slots available
for use.
--------------------------------------------------------------------------
Thank you for your help.
Alex
On Jun 24, 2015, at 10:56 AM, Alexander Tzanov <Alexander.Tzanov_at_csi.cuny.edu<mailto:Alexander.Tzanov_at_csi.cuny.edu>> wrote:
Dear all,
I am trying to run NAMD 2.10 with CUDA support on single virtual node. My CUDA is 6.5.14. I am running
on IB cluster which runs PBS pro ver. 12.1.0.131281. I want to run on a single virtual node with
4 CPU cores and 2 GPU (the CPU itself has 16 cores). I compiled NAMD with cuda support
(mpi, smp CHARMM++ underneath). However when the NAMD cannot address more than one core.
As a result I get error “ Not enough slots”. Does anyone see the problem and if so to share his/her experience.
Thank you
Alex
________________________________
Celebrate the World of Peptide Chemistry and Biology. Register today for the Symposium in Honor of the Scientific Contributions of Dr. Fred Naider><https://urldefense.proofpoint.com/v2/url?u=http-3A__www.csi.cuny.edu_symposium_&d=AwMGaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=zFfoK61upjM5BwyoRAsX8dLq7rwWm8aw7r7dqtjgcCE&m=FouggfgNdBF_Xva0RYvW6rRs3ZevGNV12nuJLKy0tfM&s=SYiHk1J-P9g3esCPzk8qAIqXOuvwX6rx2Bp951Sxcjc&e=>
________________________________
Celebrate the World of Peptide Chemistry and Biology. Register today for the Symposium in Honor of the Scientific Contributions of Dr. Fred Naider><http://www.csi.cuny.edu/symposium/>
- Next message:Baker D.J.: 'NAMD 2.10 on IBM POWER(8) machines'
- Previous message:Axel Kohlmeyer: 'Re: Re: run on sungle node'
- In reply to:Josh Vermaas: 'Re: Re: run on sungle node'
- Next in thread:Axel Kohlmeyer: 'Re: Re: run on sungle node'
- Messages sorted by:[ date ][ thread ][ subject ][ author ][ attachment ]
Mpirun There Are Not Enough Slots Available In The System To Satisfy
This archive was generated by hypermail 2.1.6 : Thu Dec 31 2015 - 23:21:56 CST