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elegant file locked on centos7 server
Posted: 03 Nov 2020, 03:45
by Hexin
I install elegant and sddstoolkit on a centos7 server without root permission by the rpm packages，
SDDSToolKit-5.0-1.rhel.7.x86_64.rpm and elegant-2020.4.0-5.rhel.7.openmpi.x86_64.rpm.
The sddstoolkits can perform normally but elegant has a file writing bug:
when I perform an example from the official website,It had a problem and reported an error:
Code: Select all
Error:
unable to open file run.acc for writing--file is locked (SDDS_InitializeOutput)
Error:
Unable to open file "run.fin" for reading (SDDS_InitializeInput)
Error:
Unable to open file "run.cen" for reading (SDDS_InitializeInput)
Error:
Unable to read layout--no header lines found (SDDS_ReadLayout)
Error:
Unable to open file "run.los" for reading (SDDS_InitializeInput)
What can I do to run elegant properly?
Hexin .
Re: elegant file locked on centos7 server
Posted: 03 Nov 2020, 11:10
by soliday
What type of file system are you writing to? ext3, ext4, NFS, lustre, gpfs or something else?
Re: elegant file locked on centos7 server
Posted: 04 Nov 2020, 06:50
by Hexin
our server file system is lustre.
Re: elegant file locked on centos7 server
Posted: 04 Nov 2020, 17:21
by michael_borland
This can sometimes happen if elegant is run by mistake using mpiexec, since in that case multiple identical instances are run.
--Michael
Re: elegant file locked on centos7 server
Posted: 05 Nov 2020, 07:16
by Hexin
I didn't use mpixec, I just ran a simple example. This example is examples / acceptance / energyscan1, which is from your website.
The RPM package of elegant and sddstoolkits installed on my PC can work normally, but file locked (SDDS_InitializeInput) problem will appear when running in our school Supercomputer Center.
The supercomputing center systecms of our school is centos7, and the file system is lustre.
What should I do to be able to use elegant properly on this system?
Re: elegant file locked on centos7 server
Posted: 05 Nov 2020, 13:28
by soliday
Is there run.acc file in that directory? Initially there isn't. So if there is, perhaps it was left behind by a previous test and left locked for some reason. What happens if you delete run.acc and try again?
Re: elegant file locked on centos7 server
Posted: 05 Nov 2020, 20:23
by Hexin
If I delete the run.acc,the error information is:
Error:
Unable to access file run.acc--file is locked (SDDS_InitializeOutput)
Re: elegant file locked on centos7 server
Posted: 05 Nov 2020, 20:33
by soliday
I am going to guess that your lustre system is not using the flock mount option:
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$ mount | grep lustre
192.168.2.153@o2ib:/anltest on /lustre type lustre (rw,noauto,flock)
I will create an RPM for you with file locking turned off.
Re: elegant file locked on centos7 server
Posted: 05 Nov 2020, 21:05
by Hexin
This is my server information of lustre：
mount | grep lustre
14.31.3.27@o2ib:/home on /home type lustre (rw,lazystatfs)
14.2.11.11@o2ib:/data on /software type lustre (rw,lazystatfs)
14.2.11.11@o2ib:/home on /project type lustre (rw,lazystatfs)
14.2.11.11@o2ib:/datasgg on /dat01 type lustre (rw,lazystatfs)
14.2.12.10@o2ib:/scratch on /scratch type lustre (rw,flock,lazystatfs)
Re: elegant file locked on centos7 server
Posted: 05 Nov 2020, 21:06
by soliday