Queue: PublicMetaMap
Subject: mmserver13 dies with SPIO_E_TOO_MANY_OPEN_FILES
Status: resolved
Created: Mon Nov 04 13:13:12 2013
Resolved: Tue Nov 05 16:44:38 2013
LastUpdated: Tue Nov 05 16:44:38 2013
Subject: mmserver13 dies with SPIO_E_TOO_MANY_OPEN_FILES
Status: resolved
Created: Mon Nov 04 13:13:12 2013
Resolved: Tue Nov 05 16:44:38 2013
LastUpdated: Tue Nov 05 16:44:38 2013
Subject:
Creator: 28
Created: 2013-11-04 18:13:12
Transaction: 1988
Parent: 0
MessageId: [email redacted]
Filename:
ContentType: text/plain
ContentEncoding: none
Content:
>Category: mmtxT
>Synopsis: mmserver13 dies with SPIO_E_TOO_MANY_OPEN_FILES
>Confidential: no
>Severity: serious
>Priority: medium
>Class: sw-bug
>Submitter-Id: mmtxWeb
>Release:
>Environment:
>Operating System - MetaMap:
>OS Version - 3.11.2-201.fc19.x86_64 (Fedora Core 19)
>Java Version - Java 1.7
>Description:
MMserver 2013 will eventually die from having too many open pipes when being called by the Java API from a remote host:
(snip)
Established connection $stream(-227805152) to WSD Server on localhost.
Established connection $stream(-227875744) to TAGGER Server on localhost.
Established connection $stream(-227875600) to WSD Server on localhost.
! [PBEANS] - prologbeans could not handle data_received('$pbstream'('$stream'(-227876488),'$stream'(-227876488))): error(system_error,system_error('SPIO_E_TOO_MANY_OPEN_FILES'))
! [PBEANS] - listen error: error(system_error,system_error('SPIO_E_TOO_MANY_OPEN_FILES'))
! System error
! 'SPIO_E_TOO_MANY_OPEN_FILES'
! System error
! 'SPIO_E_TOO_MANY_OPEN_FILES'
..and it has to be restarted. Watching the /proc//fd/ directory, pipes are created but never removed. When it hits 1000 pipes then the process dies. I could increase the FD limit but this will only delay the problem for a short while.
MMserver is running on a Fedora Core 19 VM with 8GB RAM and Sun JDK 1.7.0_45 (32-bit)
>How-To-Repeat:
Example use of Java API on Mac workstation:
MetaMapApi api = new MetaMapApiImpl(mapServer.toString())
api.resetOptions()
api.setOptions("-y -R SNOMEDCT");
map = api.processCitationsFromString(text)
(do stuff with map)
api.getSession().disconnect()
Calling the above 113 times kills mmserver with error SPIO_E_TOO_MANY_OPEN_FILES
>Unformatted:
Subject: Creator: 28 Created: 2013-11-04 21:55:37 Transaction: 1996 Parent: 0 MessageId: [email redacted] Filename: ContentType: text/html ContentEncoding: none Content: It appears that MMServer/MetaMap is retaining the pipe when calling the WSD Server. The behavior does not occur if WSD is not used.
I will have the main MetaMap developer take a look at this.
Sincerely,
Willie Rogers
On Mon Nov 04 13:13:12 2013, wjrogers wrote:
>
> >Submitter: [email redacted]
> >Category: mmtxT
> >Synopsis: mmserver13 dies with SPIO_E_TOO_MANY_OPEN_FILES
> >Confidential: no
> >Severity: serious
> >Priority: medium
> >Class: sw-bug
> >Submitter-Id: mmtxWeb
> >Originator: Joe Mesterhazy ([email redacted])
> >Release:
> >Environment:
> >Operating System - MetaMap:
> >OS Version - 3.11.2-201.fc19.x86_64 (Fedora Core 19)
> >Java Version - Java 1.7
> >Description:
> MMserver 2013 will eventually die from having too many open pipes when
> being called by the Java API from a remote host:
>
> (snip)
> Established connection $stream(-227805152) to WSD Server on localhost.
> Established connection $stream(-227875744) to TAGGER Server on
> localhost.
> Established connection $stream(-227875600) to WSD Server on localhost.
> ! [PBEANS] - prologbeans could not handle
> data_received('$pbstream'('$stream'(-227876488),'$stream'(-
> 227876488))):
> error(system_error,system_error('SPIO_E_TOO_MANY_OPEN_FILES'))
> ! [PBEANS] - listen error:
> error(system_error,system_error('SPIO_E_TOO_MANY_OPEN_FILES'))
> ! System error
> ! 'SPIO_E_TOO_MANY_OPEN_FILES'
> ! System error
> ! 'SPIO_E_TOO_MANY_OPEN_FILES'
>
> ..and it has to be restarted. Watching the /proc/<PID>/fd/ directory,
> pipes are created but never removed. When it hits 1000 pipes then
> the process dies. I could increase the FD limit but this will only
> delay the problem for a short while.
>
> MMserver is running on a Fedora Core 19 VM with 8GB RAM and Sun JDK
> 1.7.0_45 (32-bit)
>
> >How-To-Repeat:
> Example use of Java API on Mac workstation:
> MetaMapApi api = new MetaMapApiImpl(mapServer.toString())
> api.resetOptions()
> api.setOptions("-y -R SNOMEDCT");
> map = api.processCitationsFromString(text)
> (do stuff with map)
> api.getSession().disconnect()
>
> Calling the above 113 times kills mmserver with error
> SPIO_E_TOO_MANY_OPEN_FILES
>
> >Unformatted:
Subject: [PublicMetamap #50] mmserver13 dies with SPIO_E_TOO_MANY_OPEN_FILES
Creator: 1
Created: 2013-11-04 21:55:37
Transaction: 1997
Parent: 0
MessageId: [email redacted]
Filename:
ContentType: text/plain
ContentEncoding: none
Content: It appears that MMServer/MetaMap is retaining the pipe when calling the WSD
Server. The behavior does not occur if WSD is not used.
I will have the main MetaMap developer take a look at this.
Sincerely,
Willie Rogers
On Mon Nov 04 13:13:12 2013, wjrogers wrote:
>
> >Category: mmtxT
> >Synopsis: mmserver13 dies with SPIO_E_TOO_MANY_OPEN_FILES
> >Confidential: no
> >Severity: serious
> >Priority: medium
> >Class: sw-bug
> >Submitter-Id: mmtxWeb
> >Release:
> >Environment:
> >Operating System - MetaMap:
> >OS Version - 3.11.2-201.fc19.x86_64 (Fedora Core 19)
> >Java Version - Java 1.7
> >Description:
> MMserver 2013 will eventually die from having too many open pipes when
> being called by the Java API from a remote host:
>
> (snip)
> Established connection $stream(-227805152) to WSD Server on localhost.
> Established connection $stream(-227875744) to TAGGER Server on
> localhost.
> Established connection $stream(-227875600) to WSD Server on localhost.
> ! [PBEANS] - prologbeans could not handle
> data_received('$pbstream'('$stream'(-227876488),'$stream'(-
> 227876488))):
> error(system_error,system_error('SPIO_E_TOO_MANY_OPEN_FILES'))
> ! [PBEANS] - listen error:
> error(system_error,system_error('SPIO_E_TOO_MANY_OPEN_FILES'))
> ! System error
> ! 'SPIO_E_TOO_MANY_OPEN_FILES'
> ! System error
> ! 'SPIO_E_TOO_MANY_OPEN_FILES'
>
> ..and it has to be restarted. Watching the /proc//fd/ directory,
> pipes are created but never removed. When it hits 1000 pipes then
> the process dies. I could increase the FD limit but this will only
> delay the problem for a short while.
>
> MMserver is running on a Fedora Core 19 VM with 8GB RAM and Sun JDK
> 1.7.0_45 (32-bit)
>
> >How-To-Repeat:
> Example use of Java API on Mac workstation:
> MetaMapApi api = new MetaMapApiImpl(mapServer.toString())
> api.resetOptions()
> api.setOptions("-y -R SNOMEDCT");
> map = api.processCitationsFromString(text)
> (do stuff with map)
> api.getSession().disconnect()
>
> Calling the above 113 times kills mmserver with error
> SPIO_E_TOO_MANY_OPEN_FILES
>
> >Unformatted:
Subject: [PublicMetamap #50] mmserver13 dies with SPIO_E_TOO_MANY_OPEN_FILES
Creator: 1
Created: 2013-11-04 21:55:37
Transaction: 1998
Parent: 0
MessageId: [email redacted]
Filename:
ContentType: text/plain
ContentEncoding: none
Content: It appears that MMServer/MetaMap is retaining the pipe when calling the WSD
Server. The behavior does not occur if WSD is not used.
I will have the main MetaMap developer take a look at this.
Sincerely,
Willie Rogers
On Mon Nov 04 13:13:12 2013, wjrogers wrote:
>
> >Category: mmtxT
> >Synopsis: mmserver13 dies with SPIO_E_TOO_MANY_OPEN_FILES
> >Confidential: no
> >Severity: serious
> >Priority: medium
> >Class: sw-bug
> >Submitter-Id: mmtxWeb
> >Release:
> >Environment:
> >Operating System - MetaMap:
> >OS Version - 3.11.2-201.fc19.x86_64 (Fedora Core 19)
> >Java Version - Java 1.7
> >Description:
> MMserver 2013 will eventually die from having too many open pipes when
> being called by the Java API from a remote host:
>
> (snip)
> Established connection $stream(-227805152) to WSD Server on localhost.
> Established connection $stream(-227875744) to TAGGER Server on
> localhost.
> Established connection $stream(-227875600) to WSD Server on localhost.
> ! [PBEANS] - prologbeans could not handle
> data_received('$pbstream'('$stream'(-227876488),'$stream'(-
> 227876488))):
> error(system_error,system_error('SPIO_E_TOO_MANY_OPEN_FILES'))
> ! [PBEANS] - listen error:
> error(system_error,system_error('SPIO_E_TOO_MANY_OPEN_FILES'))
> ! System error
> ! 'SPIO_E_TOO_MANY_OPEN_FILES'
> ! System error
> ! 'SPIO_E_TOO_MANY_OPEN_FILES'
>
> ..and it has to be restarted. Watching the /proc//fd/ directory,
> pipes are created but never removed. When it hits 1000 pipes then
> the process dies. I could increase the FD limit but this will only
> delay the problem for a short while.
>
> MMserver is running on a Fedora Core 19 VM with 8GB RAM and Sun JDK
> 1.7.0_45 (32-bit)
>
> >How-To-Repeat:
> Example use of Java API on Mac workstation:
> MetaMapApi api = new MetaMapApiImpl(mapServer.toString())
> api.resetOptions()
> api.setOptions("-y -R SNOMEDCT");
> map = api.processCitationsFromString(text)
> (do stuff with map)
> api.getSession().disconnect()
>
> Calling the above 113 times kills mmserver with error
> SPIO_E_TOO_MANY_OPEN_FILES
>
> >Unformatted:
Subject: Creator: 28 Created: 2013-11-05 21:44:37 Transaction: 2000 Parent: 0 MessageId: [email redacted] Filename: ContentType: text/html ContentEncoding: none Content: After consulting the lead MetaMap developer, I've built a new mmserver binary which does NOT re-open the WSD server repeatedly. There is a caveat however,
once you set the WSD option (-y) in mmserver, it cannot be unset.
The macosx and linux distributions with the new binaries are available at:
http://metamap.nlm.nih.gov/download/public_mm_darwin_javaapi_2013.tar.bz2
http://metamap.nlm.nih.gov/download/public_mm_linux_javaapi_2013.tar.bz2
MD5 checksums for the new archives are:
e5a046f4c7e194b247ec6af275124caa public_mm_darwin_javaapi_2013.tar.bz2
09132d9d0bf31eacfab8851295ed91a2 public_mm_linux_javaapi_2013.tar.bz2
Sincerely,
Willie Rogers
Subject: [PublicMetamap #50] mmserver13 dies with SPIO_E_TOO_MANY_OPEN_FILES
Creator: 1
Created: 2013-11-05 21:44:38
Transaction: 2001
Parent: 0
MessageId: [email redacted]
Filename:
ContentType: text/plain
ContentEncoding: none
Content: After consulting the lead MetaMap developer, I've built a new mmserver binary
which does NOT re-open the WSD server repeatedly. There is a caveat however,
once you set the WSD option (-y) in mmserver, it cannot be unset.
The macosx and linux distributions with the new binaries are available at:
http://metamap.nlm.nih.gov/download/public_mm_darwin_javaapi_2013.tar.bz2
http://metamap.nlm.nih.gov/download/public_mm_linux_javaapi_2013.tar.bz2
MD5 checksums for the new archives are:
e5a046f4c7e194b247ec6af275124caa public_mm_darwin_javaapi_2013.tar.bz2
09132d9d0bf31eacfab8851295ed91a2 public_mm_linux_javaapi_2013.tar.bz2
Sincerely,
Willie Rogers