recon-all in 7.0.0-beta: /usr/bin/time not installed on server, failed many hours into run
External Email - Use Caution
Hello all!
A cautionary tale between versions 6.0.0 and 7.0.0. I was running recon-all as I was with version 6.0.0 and found that my runs would fail on our hpc after failing to find /usr/bin/time. This would leave it in "is-running" state. I am currently awaiting the installation of the standalone /usr/bin/time on our server and will run recon-all to see if this resolves the issue. Attached is the full log, ending with the hard exit error.
Best.
BR
--
Brian Renner, MD Research Associate, Neurology brian.renner@cshs.orgmailto:brian.renner@cshs.org
Cedars-Sinai 127 S. San Vicente Blvd, Suite A6600 : Los Angeles CA 90048 office 310-423-1589 : mobile 310-658-3492 : cedars-sinai.orghttps://www.cedars-sinai.org/
IMPORTANT WARNING: This message is intended for the use of the person or entity to which it is addressed and may contain information that is privileged and confidential, the disclosure of which is governed by applicable law. If the reader of this message is not the intended recipient, or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this information is strictly prohibited. Thank you for your cooperation.
In v7, fs_time runs by default to keep track of exec time and resources used. You can turn it off by setting the FS_TIME_ALLOW env var to 0
On 4/16/2020 5:03 PM, Renner, Brian wrote:
External Email - Use Caution
Hello all!
A cautionary tale between versions 6.0.0 and 7.0.0. I was running recon-all as I was with version 6.0.0 and found that my runs would fail on our hpc after failing to find /usr/bin/time. This would leave it in "is-running" state. I am currently awaiting the installation of the standalone /usr/bin/time on our server and will run recon-all to see if this resolves the issue. Attached is the full log, ending with the hard exit error.
Best.
BR
**--*
*Brian Renner, MD* *Research Associate, Neurology * brian.renner@cshs.org mailto:brian.renner@cshs.org
*Cedars-Sinai* 127 S. San Vicente Blvd, Suite A6600 : Los Angeles CA 90048 office 310-423-1589 : mobile 310-658-3492 : cedars-sinai.org https://www.cedars-sinai.org/
IMPORTANT WARNING: This message is intended for the use of the person or entity to which it is addressed and may contain information that is privileged and confidential, the disclosure of which is governed by applicable law. If the reader of this message is not the intended recipient, or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this information is strictly prohibited. Thank you for your cooperation.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
In that log file you sent, it doesn’t seem to include any hard errors. Is it just the stdout log? Can you send the recon-all.log?
Thanks Andrew
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Douglas N. Greve" dgreve@mgh.harvard.edu Reply-To: FS Help freesurfer@nmr.mgh.harvard.edu Date: Thursday, April 16, 2020 at 5:10 PM To: FS Help freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] recon-all in 7.0.0-beta: /usr/bin/time not installed on server, failed many hours into run
In v7, fs_time runs by default to keep track of exec time and resources used. You can turn it off by setting the FS_TIME_ALLOW env var to 0
On 4/16/2020 5:03 PM, Renner, Brian wrote:
External Email - Use Caution Hello all!
A cautionary tale between versions 6.0.0 and 7.0.0. I was running recon-all as I was with version 6.0.0 and found that my runs would fail on our hpc after failing to find /usr/bin/time. This would leave it in "is-running" state. I am currently awaiting the installation of the standalone /usr/bin/time on our server and will run recon-all to see if this resolves the issue. Attached is the full log, ending with the hard exit error.
Best.
BR
--
Brian Renner, MD Research Associate, Neurology brian.renner@cshs.orgmailto:brian.renner@cshs.org
Cedars-Sinai 127 S. San Vicente Blvd, Suite A6600 : Los Angeles CA 90048 office 310-423-1589 : mobile 310-658-3492 : cedars-sinai.orghttps://www.cedars-sinai.org/
IMPORTANT WARNING: This message is intended for the use of the person or entity to which it is addressed and may contain information that is privileged and confidential, the disclosure of which is governed by applicable law. If the reader of this message is not the intended recipient, or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this information is strictly prohibited. Thank you for your cooperation.
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Good morning, Andrew!
The log was attached in the original message as "fs_hc.o14820". I've re-attached another, similar, log to this to this email as "fs_hc.o13944". The hard error is the very last line, and pithy, thankfully! As shown below:
ERROR: cannot find /usr/bin/time
BR ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Hoopes, Andrew AHOOPES@mgh.harvard.edu Sent: Thursday, April 16, 2020 2:35 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: [External] Re: [Freesurfer] recon-all in 7.0.0-beta: /usr/bin/time not installed on server, failed many hours into run
In that log file you sent, it doesn’t seem to include any hard errors. Is it just the stdout log? Can you send the recon-all.log?
Thanks
Andrew
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Douglas N. Greve" dgreve@mgh.harvard.edu Reply-To: FS Help freesurfer@nmr.mgh.harvard.edu Date: Thursday, April 16, 2020 at 5:10 PM To: FS Help freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] recon-all in 7.0.0-beta: /usr/bin/time not installed on server, failed many hours into run
In v7, fs_time runs by default to keep track of exec time and resources used. You can turn it off by setting the FS_TIME_ALLOW env var to 0
On 4/16/2020 5:03 PM, Renner, Brian wrote:
External Email - Use Caution
Hello all!
A cautionary tale between versions 6.0.0 and 7.0.0. I was running recon-all as I was with version 6.0.0 and found that my runs would fail on our hpc after failing to find /usr/bin/time. This would leave it in "is-running" state. I am currently awaiting the installation of the standalone /usr/bin/time on our server and will run recon-all to see if this resolves the issue. Attached is the full log, ending with the hard exit error.
Best.
BR
--
Brian Renner, MD Research Associate, Neurology brian.renner@cshs.orgmailto:brian.renner@cshs.org
Cedars-Sinai 127 S. San Vicente Blvd, Suite A6600 : Los Angeles CA 90048 office 310-423-1589 : mobile 310-658-3492 : cedars-sinai.orghttps://www.cedars-sinai.org/
IMPORTANT WARNING: This message is intended for the use of the person or entity to which it is addressed and may contain information that is privileged and confidential, the disclosure of which is governed by applicable law. If the reader of this message is not the intended recipient, or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this information is strictly prohibited. Thank you for your cooperation.
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
As long as you're investigating this -- I have a related problem using the FS v7 beta version with a Mac OS vs. Cent OS.
When the "time -o" flag is used on the Mac -- it doesn't recognize the "-o" flag and fails. "/usr/bin/time: illegal option -- o usage: time [-lp] command." See the attached recon-all.log. I believe the recommendation is to install gnu-time and use "gtime" on a Mac if the intention is to use the "-o" flag. The only flags the Mac version of time recognizes are -l and -p.
I have no such troubles on our HPC with CentOS, as the time function has the standard GNU options -f -p -o -a -v.
-Adam
On Fri, Apr 17, 2020 at 11:45 AM Renner, Brian Brian.Renner@cshs.org wrote:
External Email - Use CautionGood morning, Andrew!
The log was attached in the original message as "fs_hc.o14820". I've re-attached another, similar, log to this to this email as "fs_hc.o13944". The hard error is the very last line, and pithy, thankfully! As shown below:
ERROR: cannot find /usr/bin/time
BR
*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Hoopes, Andrew < AHOOPES@mgh.harvard.edu> *Sent:* Thursday, April 16, 2020 2:35 PM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject:* [External] Re: [Freesurfer] recon-all in 7.0.0-beta: /usr/bin/time not installed on server, failed many hours into run
In that log file you sent, it doesn’t seem to include any hard errors. Is it just the stdout log? Can you send the recon-all.log?
Thanks
Andrew
*From: *freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Douglas N. Greve" dgreve@mgh.harvard.edu *Reply-To: *FS Help freesurfer@nmr.mgh.harvard.edu *Date: *Thursday, April 16, 2020 at 5:10 PM *To: *FS Help freesurfer@nmr.mgh.harvard.edu *Subject: *Re: [Freesurfer] recon-all in 7.0.0-beta: /usr/bin/time not installed on server, failed many hours into run
In v7, fs_time runs by default to keep track of exec time and resources used. You can turn it off by setting the FS_TIME_ALLOW env var to 0
On 4/16/2020 5:03 PM, Renner, Brian wrote:
External Email - Use Caution *Hello all!
A cautionary tale between versions 6.0.0 and 7.0.0. I was running recon-all as I was with version 6.0.0 and found that my runs would fail on our hpc after failing to find /usr/bin/time. This would leave it in "is-running" state. I am currently awaiting the installation of the standalone /usr/bin/time on our server and will run recon-all to see if this resolves the issue. Attached is the full log, ending with the hard exit error.
Best.
BR
--
*Brian Renner, MD* *Research Associate, Neurology * brian.renner@cshs.org
*Cedars-Sinai* 127 S. San Vicente Blvd, Suite A6600 : Los Angeles CA 90048 office 310-423-1589 : mobile 310-658-3492 : cedars-sinai.org https://www.cedars-sinai.org/
IMPORTANT WARNING: This message is intended for the use of the person or entity to which it is addressed and may contain information that is privileged and confidential, the disclosure of which is governed by applicable law. If the reader of this message is not the intended recipient, or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this information is strictly prohibited. Thank you for your cooperation.
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Okay, thanks for the info! Recon-all usually checks to make sure fs_time is valid before running it, but there was one step (mris_remesh) where it was calling fs_time unconditionally. This has been fixed in dev and will be in the upcoming release. Also, fs_time is not expected to run correctly on osx and will be disabled by recon-all.
best Andrew
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Adam Martersteck acmarter@gmail.com Reply-To: FS Help freesurfer@nmr.mgh.harvard.edu Date: Friday, April 17, 2020 at 1:21 PM To: FS Help freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] [External] Re: recon-all in 7.0.0-beta: /usr/bin/time not installed on server, failed many hours into run
External Email - Use Caution As long as you're investigating this -- I have a related problem using the FS v7 beta version with a Mac OS vs. Cent OS.
When the "time -o" flag is used on the Mac -- it doesn't recognize the "-o" flag and fails. "/usr/bin/time: illegal option -- o usage: time [-lp] command." See the attached recon-all.log. I believe the recommendation is to install gnu-time and use "gtime" on a Mac if the intention is to use the "-o" flag. The only flags the Mac version of time recognizes are -l and -p.
I have no such troubles on our HPC with CentOS, as the time function has the standard GNU options -f -p -o -a -v.
-Adam
On Fri, Apr 17, 2020 at 11:45 AM Renner, Brian <Brian.Renner@cshs.orgmailto:Brian.Renner@cshs.org> wrote:
External Email - Use Caution Good morning, Andrew!
The log was attached in the original message as "fs_hc.o14820". I've re-attached another, similar, log to this to this email as "fs_hc.o13944". The hard error is the very last line, and pithy, thankfully! As shown below:
ERROR: cannot find /usr/bin/time
BR ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Hoopes, Andrew <AHOOPES@mgh.harvard.edumailto:AHOOPES@mgh.harvard.edu> Sent: Thursday, April 16, 2020 2:35 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [External] Re: [Freesurfer] recon-all in 7.0.0-beta: /usr/bin/time not installed on server, failed many hours into run
In that log file you sent, it doesn’t seem to include any hard errors. Is it just the stdout log? Can you send the recon-all.log?
Thanks
Andrew
From: <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Douglas N. Greve" <dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu> Reply-To: FS Help <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Thursday, April 16, 2020 at 5:10 PM To: FS Help <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] recon-all in 7.0.0-beta: /usr/bin/time not installed on server, failed many hours into run
In v7, fs_time runs by default to keep track of exec time and resources used. You can turn it off by setting the FS_TIME_ALLOW env var to 0
On 4/16/2020 5:03 PM, Renner, Brian wrote:
External Email - Use Caution
Hello all!
A cautionary tale between versions 6.0.0 and 7.0.0. I was running recon-all as I was with version 6.0.0 and found that my runs would fail on our hpc after failing to find /usr/bin/time. This would leave it in "is-running" state. I am currently awaiting the installation of the standalone /usr/bin/time on our server and will run recon-all to see if this resolves the issue. Attached is the full log, ending with the hard exit error.
Best.
BR
--
Brian Renner, MD Research Associate, Neurology brian.renner@cshs.orgmailto:brian.renner@cshs.org
Cedars-Sinai 127 S. San Vicente Blvd, Suite A6600 : Los Angeles CA 90048 office 310-423-1589 : mobile 310-658-3492 : cedars-sinai.orghttps://www.cedars-sinai.org/
IMPORTANT WARNING: This message is intended for the use of the person or entity to which it is addressed and may contain information that is privileged and confidential, the disclosure of which is governed by applicable law. If the reader of this message is not the intended recipient, or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this information is strictly prohibited. Thank you for your cooperation.
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Adam Martersteck -
Douglas N. Greve -
Hoopes, Andrew -
Renner, Brian