[Met_help] [rt.rap.ucar.edu #90135] History for commands to execute within MET container? (UNCLASSIFIED)
John Halley Gotway via RT
met_help at ucar.edu
Fri May 10 12:07:45 MDT 2019
----------------------------------------------------------------
Initial Request
----------------------------------------------------------------
CLASSIFICATION: UNCLASSIFIED
I pulled the METV8.0 docker image from dtcenter and converted it into a
singularity image on the ARL HPC and am trying to execute the command within
the container. It doesn't seem to accept the command "point_stat". See
following dialog for two separate attempts before I figured it was looking
for a specific command to execute:
-bash-4.2$ singularity exec met-8.0.simg
ERROR : No program name to exec
ABORT : Retval = 255
-bash-4.2$ singularity exec point_stat
ERROR : Image path point_stat doesn't exist: No such file or directory
ABORT : Retval = 255
Could you provide some commands which would normally execute?
Thanks.
R/
John
Mr. John W. Raby
U.S. Army Research Laboratory
White Sands Missile Range, NM 88002
(575) 678-2004 DSN 258-2004
FAX (575) 678-1230 DSN 258-1230
Email: john.w.raby2.civ at mail.mil
CLASSIFICATION: UNCLASSIFIED
----------------------------------------------------------------
Complete Ticket History
----------------------------------------------------------------
Subject: commands to execute within MET container? (UNCLASSIFIED)
From: John Halley Gotway
Time: Wed May 08 15:36:13 2019
Hi John,
I see that you have a question about using the MET docker containers.
You
ultimately want to use them in singularity, but I don't have
singularity
available on my machine. So let me offer some basic docker commands
to see
if that helps.
(1) I'm starting with no docker images on my machine:
*vpn2:~ johnhg$ docker images*
*REPOSITORY TAG IMAGE ID CREATED
SIZE*
(2) Use docker pull to get the met/8.1 image:
*docker pull dtcenter/met-8.1*
(3) See that it's now on my machine:
*vpn2:~ johnhg$ docker images*
*REPOSITORY TAG IMAGE ID CREATED
SIZE*
*dtcenter/met 8.1 c78d804fa826 2 days
ago
2.28GB*
(3) Use docker run to "log into" a met/8.1 container and run 'which'
to
find point_stat.
*vpn2:~ johnhg$ docker run -it --rm dtcenter/met:8.1 /bin/bash*
*[root at 0df0f740d1aa met]# which point_stat*
*/usr/local/bin/point_stat*
*exit*
This demonstrates that point_stat can be found in
/usr/local/bin/point_stat
inside the container.
(4) Run a container to see the usage statement for point-stat:
*vpn2:~ johnhg$ docker run -it --rm dtcenter/met:8.1
/usr/local/bin/point_stat*
**** Model Evaluation Tools (METV8.1) ****
*Usage: point_stat*
* fcst_file*
*... the rest of the usage statement ...*
Hope that helps.
Thanks,
John Halley Gotway
On Wed, May 8, 2019 at 3:08 PM Raby, John W USA CIV via RT <
met_help at ucar.edu> wrote:
>
> Wed May 08 15:07:52 2019: Request 90135 was acted upon.
> Transaction: Ticket created by john.w.raby2.civ at mail.mil
> Queue: met_help
> Subject: commands to execute within MET container?
(UNCLASSIFIED)
> Owner: Nobody
> Requestors: john.w.raby2.civ at mail.mil
> Status: new
> Ticket <URL:
https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=90135 >
>
>
> CLASSIFICATION: UNCLASSIFIED
>
> I pulled the METV8.0 docker image from dtcenter and converted it
into a
> singularity image on the ARL HPC and am trying to execute the
command
> within
> the container. It doesn't seem to accept the command "point_stat".
See
> following dialog for two separate attempts before I figured it was
looking
> for a specific command to execute:
>
> -bash-4.2$ singularity exec met-8.0.simg
> ERROR : No program name to exec
> ABORT : Retval = 255
> -bash-4.2$ singularity exec point_stat
> ERROR : Image path point_stat doesn't exist: No such file or
directory
> ABORT : Retval = 255
>
> Could you provide some commands which would normally execute?
>
> Thanks.
>
> R/
> John
>
> Mr. John W. Raby
> U.S. Army Research Laboratory
> White Sands Missile Range, NM 88002
> (575) 678-2004 DSN 258-2004
> FAX (575) 678-1230 DSN 258-1230
> Email: john.w.raby2.civ at mail.mil
>
>
> CLASSIFICATION: UNCLASSIFIED
>
>
------------------------------------------------
Subject: commands to execute within MET container? (UNCLASSIFIED)
From: Raby, John W USA CIV
Time: Wed May 08 16:37:33 2019
CLASSIFICATION: UNCLASSIFIED
John -
Thanks for leading me in this direction. I looked at (3) below and was
able to
see the usage for point_stat by applying a similar approach but with
Singularity flavor.
In the directory where I have the MET singularity image (met-8.0.simg
) I
executed the following run command:
-bash-4.2$ ll
total 537420
-rwxr-xr-x. 1 jraby 1487I100 550309919 May 8 13:52 met-8.0.simg
-bash-4.2$ singularity run met-8.0.simg
There was no response, but when I executed a which command it provided
the
path to point_stat:
bash-4.2$ which point_stat
/usr/local/bin/point_stat
Then I ran the command to see the usage per your step (4):
bash-4.2$ /usr/local/bin/point_stat
*** Model Evaluation Tools (METV8.0) ***
Usage: point_stat
fcst_file
obs_file
config_file
[-point_obs file]
[-obs_valid_beg time]
[-obs_valid_end time]
[-outdir path]
[-log file]
[-v level]
where "fcst_file" is a gridded forecast file containing the
field(s)
to be verified (required).
"obs_file" is an observation file in NetCDF format
containing
the verifying point observations (required).
"config_file" is a PointStatConfig file containing the
desired
configuration settings (required).
"-point_obs file" specifies additional NetCDF point
observation files to be used (optional).
"-obs_valid_beg time" in YYYYMMDD[_HH[MMSS]] sets the
beginning of the matching time window (optional).
"-obs_valid_end time" in YYYYMMDD[_HH[MMSS]] sets the
end of
the matching time window (optional).
"-outdir path" overrides the default output directory
(.)
(optional).
"-log file" outputs log messages to the specified file
(optional).
"-v level" overrides the default level of logging (2)
(optional).
Making progress!
R/
John
-----Original Message-----
From: John Halley Gotway via RT [mailto:met_help at ucar.edu]
Sent: Wednesday, May 8, 2019 3:36 PM
To: Raby, John W CIV USARMY CCDC ARL (USA) <john.w.raby2.civ at mail.mil>
Cc: Dawson, Leelinda P CIV USARMY CCDC ARL (USA)
<leelinda.p.dawson.civ at mail.mil>
Subject: [Non-DoD Source] Re: [rt.rap.ucar.edu #90135] commands to
execute
within MET container? (UNCLASSIFIED)
All active links contained in this email were disabled. Please verify
the
identity of the sender, and confirm the authenticity of all links
contained
within the message prior to copying and pasting the address to a Web
browser.
----
Hi John,
I see that you have a question about using the MET docker containers.
You
ultimately want to use them in singularity, but I don't have
singularity
available on my machine. So let me offer some basic docker commands
to see if
that helps.
(1) I'm starting with no docker images on my machine:
*vpn2:~ johnhg$ docker images*
*REPOSITORY TAG IMAGE ID CREATED
SIZE*
(2) Use docker pull to get the met/8.1 image:
*docker pull dtcenter/met-8.1*
(3) See that it's now on my machine:
*vpn2:~ johnhg$ docker images*
*REPOSITORY TAG IMAGE ID CREATED
SIZE*
*dtcenter/met 8.1 c78d804fa826 2 days
ago
2.28GB*
(3) Use docker run to "log into" a met/8.1 container and run 'which'
to find
point_stat.
*vpn2:~ johnhg$ docker run -it --rm dtcenter/met:8.1 /bin/bash*
*[root at 0df0f740d1aa met]# which point_stat*
*/usr/local/bin/point_stat*
*exit*
This demonstrates that point_stat can be found in
/usr/local/bin/point_stat
inside the container.
(4) Run a container to see the usage statement for point-stat:
*vpn2:~ johnhg$ docker run -it --rm dtcenter/met:8.1
/usr/local/bin/point_stat*
**** Model Evaluation Tools (METV8.1) ****
*Usage: point_stat*
* fcst_file*
*... the rest of the usage statement ...*
Hope that helps.
Thanks,
John Halley Gotway
On Wed, May 8, 2019 at 3:08 PM Raby, John W USA CIV via RT <
met_help at ucar.edu> wrote:
>
> Wed May 08 15:07:52 2019: Request 90135 was acted upon.
> Transaction: Ticket created by john.w.raby2.civ at mail.mil
> Queue: met_help
> Subject: commands to execute within MET container?
(UNCLASSIFIED)
> Owner: Nobody
> Requestors: john.w.raby2.civ at mail.mil
> Status: new
> Ticket <Caution-url:
> Caution-https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=90135 >
>
>
> CLASSIFICATION: UNCLASSIFIED
>
> I pulled the METV8.0 docker image from dtcenter and converted it
into
> a singularity image on the ARL HPC and am trying to execute the
> command within the container. It doesn't seem to accept the command
> "point_stat". See following dialog for two separate attempts before
I
> figured it was looking for a specific command to execute:
>
> -bash-4.2$ singularity exec met-8.0.simg ERROR : No program name
to
> exec ABORT : Retval = 255 -bash-4.2$ singularity exec point_stat
> ERROR : Image path point_stat doesn't exist: No such file or
> directory ABORT : Retval = 255
>
> Could you provide some commands which would normally execute?
>
> Thanks.
>
> R/
> John
>
> Mr. John W. Raby
> U.S. Army Research Laboratory
> White Sands Missile Range, NM 88002
> (575) 678-2004 DSN 258-2004
> FAX (575) 678-1230 DSN 258-1230
> Email: john.w.raby2.civ at mail.mil
>
>
> CLASSIFICATION: UNCLASSIFIED
>
>
CLASSIFICATION: UNCLASSIFIED
------------------------------------------------
Subject: commands to execute within MET container? (UNCLASSIFIED)
From: John Halley Gotway
Time: Fri May 10 12:07:30 2019
John,
Great, glad you were able to get going. If you'd like additional
examples
of running commands with a container, I'd refer you to the DTC NWP
container tutorial:
https://dtcenter.org/community-code/numerical-weather-prediction-nwp-
containers/end-end-nwp-container-online-tutorial
I think I've answered your original question, so I'll go ahead and
resolve
this ticket.
Have a nice weekend.
John
On Wed, May 8, 2019 at 4:38 PM Raby, John W USA CIV via RT <
met_help at ucar.edu> wrote:
>
> <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=90135 >
>
> CLASSIFICATION: UNCLASSIFIED
>
> John -
>
> Thanks for leading me in this direction. I looked at (3) below and
was
> able to
> see the usage for point_stat by applying a similar approach but with
> Singularity flavor.
>
> In the directory where I have the MET singularity image (met-
8.0.simg ) I
> executed the following run command:
>
> -bash-4.2$ ll
> total 537420
> -rwxr-xr-x. 1 jraby 1487I100 550309919 May 8 13:52 met-8.0.simg
> -bash-4.2$ singularity run met-8.0.simg
>
> There was no response, but when I executed a which command it
provided the
> path to point_stat:
>
> bash-4.2$ which point_stat
> /usr/local/bin/point_stat
>
>
> Then I ran the command to see the usage per your step (4):
>
> bash-4.2$ /usr/local/bin/point_stat
>
> *** Model Evaluation Tools (METV8.0) ***
>
> Usage: point_stat
> fcst_file
> obs_file
> config_file
> [-point_obs file]
> [-obs_valid_beg time]
> [-obs_valid_end time]
> [-outdir path]
> [-log file]
> [-v level]
>
> where "fcst_file" is a gridded forecast file containing
the
> field(s)
> to be verified (required).
> "obs_file" is an observation file in NetCDF format
> containing
> the verifying point observations (required).
> "config_file" is a PointStatConfig file containing
the
> desired
> configuration settings (required).
> "-point_obs file" specifies additional NetCDF point
> observation files to be used (optional).
> "-obs_valid_beg time" in YYYYMMDD[_HH[MMSS]] sets
the
> beginning of the matching time window (optional).
> "-obs_valid_end time" in YYYYMMDD[_HH[MMSS]] sets
the end
> of
> the matching time window (optional).
> "-outdir path" overrides the default output
directory (.)
> (optional).
> "-log file" outputs log messages to the specified
file
> (optional).
> "-v level" overrides the default level of logging
(2)
> (optional).
>
> Making progress!
>
> R/
> John
>
>
>
> -----Original Message-----
> From: John Halley Gotway via RT [mailto:met_help at ucar.edu]
> Sent: Wednesday, May 8, 2019 3:36 PM
> To: Raby, John W CIV USARMY CCDC ARL (USA)
<john.w.raby2.civ at mail.mil>
> Cc: Dawson, Leelinda P CIV USARMY CCDC ARL (USA)
> <leelinda.p.dawson.civ at mail.mil>
> Subject: [Non-DoD Source] Re: [rt.rap.ucar.edu #90135] commands to
> execute
> within MET container? (UNCLASSIFIED)
>
> All active links contained in this email were disabled. Please
verify the
> identity of the sender, and confirm the authenticity of all links
> contained
> within the message prior to copying and pasting the address to a Web
> browser.
>
>
>
>
> ----
>
> Hi John,
>
> I see that you have a question about using the MET docker
containers. You
> ultimately want to use them in singularity, but I don't have
singularity
> available on my machine. So let me offer some basic docker commands
to
> see if
> that helps.
>
> (1) I'm starting with no docker images on my machine:
>
> *vpn2:~ johnhg$ docker images*
>
> *REPOSITORY TAG IMAGE ID CREATED
> SIZE*
>
>
> (2) Use docker pull to get the met/8.1 image:
>
>
> *docker pull dtcenter/met-8.1*
>
>
> (3) See that it's now on my machine:
>
>
> *vpn2:~ johnhg$ docker images*
>
> *REPOSITORY TAG IMAGE ID CREATED
> SIZE*
>
> *dtcenter/met 8.1 c78d804fa826 2 days
ago
> 2.28GB*
>
>
> (3) Use docker run to "log into" a met/8.1 container and run 'which'
to
> find
> point_stat.
>
>
> *vpn2:~ johnhg$ docker run -it --rm dtcenter/met:8.1 /bin/bash*
>
> *[root at 0df0f740d1aa met]# which point_stat*
>
> */usr/local/bin/point_stat*
>
> *exit*
>
>
> This demonstrates that point_stat can be found in
> /usr/local/bin/point_stat
> inside the container.
>
>
> (4) Run a container to see the usage statement for point-stat:
>
>
> *vpn2:~ johnhg$ docker run -it --rm dtcenter/met:8.1
> /usr/local/bin/point_stat*
>
>
> **** Model Evaluation Tools (METV8.1) ****
>
>
> *Usage: point_stat*
>
> * fcst_file*
>
> *... the rest of the usage statement ...*
>
>
> Hope that helps.
>
>
> Thanks,
> John Halley Gotway
>
>
>
>
> On Wed, May 8, 2019 at 3:08 PM Raby, John W USA CIV via RT <
> met_help at ucar.edu> wrote:
>
> >
> > Wed May 08 15:07:52 2019: Request 90135 was acted upon.
> > Transaction: Ticket created by john.w.raby2.civ at mail.mil
> > Queue: met_help
> > Subject: commands to execute within MET container?
(UNCLASSIFIED)
> > Owner: Nobody
> > Requestors: john.w.raby2.civ at mail.mil
> > Status: new
> > Ticket <Caution-url:
> > Caution-https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=90135 >
> >
> >
> > CLASSIFICATION: UNCLASSIFIED
> >
> > I pulled the METV8.0 docker image from dtcenter and converted it
into
> > a singularity image on the ARL HPC and am trying to execute the
> > command within the container. It doesn't seem to accept the
command
> > "point_stat". See following dialog for two separate attempts
before I
> > figured it was looking for a specific command to execute:
> >
> > -bash-4.2$ singularity exec met-8.0.simg ERROR : No program name
to
> > exec ABORT : Retval = 255 -bash-4.2$ singularity exec point_stat
> > ERROR : Image path point_stat doesn't exist: No such file or
> > directory ABORT : Retval = 255
> >
> > Could you provide some commands which would normally execute?
> >
> > Thanks.
> >
> > R/
> > John
> >
> > Mr. John W. Raby
> > U.S. Army Research Laboratory
> > White Sands Missile Range, NM 88002
> > (575) 678-2004 DSN 258-2004
> > FAX (575) 678-1230 DSN 258-1230
> > Email: john.w.raby2.civ at mail.mil
> >
> >
> > CLASSIFICATION: UNCLASSIFIED
> >
> >
>
> CLASSIFICATION: UNCLASSIFIED
>
>
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