Hi all, I am trying to make a simple density projection of my data using yt on kraken. I have done this successfully many times before both on kraken and other machines, but lately I have been getting errors on kraken. I tried to run it interactively and it worked, but when I submit it as a job, I get this error: P000 yt : [INFO ] 2012-02-24 03:40:43,722 Created plot collection with default plot-center = [0.50027465 8203125, 0.500335693359375, 0.499969482421875] Traceback (most recent call last): File "/var/spool/alps/8952326/try1.py", line 8, in <module> profile("Feb2012/cluster_64/",imax=20) File "/lustre/scratch/yuan/enzo_yt/cluster256_nog/yuan.py", line 23, in profile File "/lustre/scratch/yuan/enzo_yt/cluster256_nog/yuan.py", line 23, in profile pc.add_projection("Density", 0) File "/lustre/scratch/proj/sw/yt/dev/lib/python2.7/site-packages/yt-2.4dev-py2.7-linux-x86_64.egg/yt/visua lization/plot_collection.py", line 758, in add_projection P000 yt : [INFO ] 2012-02-24 03:40:43,919 Starting 'Projecting level 0 / 8 ' **field_parameters) **field_parameters) File "/lustre/scratch/proj/sw/yt/dev/lib/python2.7/site-packages/yt-2.4dev-py2.7-linux-x86_64. egg/yt/data_objects/data_containers.py", line 1648, in __init__ File "/lustre/scratch/proj/sw/yt/dev/lib/python2.7/site-packages/yt-2.4dev-py2.7-linux-x86_64.egg/yt/data_ objects/data_containers.py", line 309, in _refresh_data ....... File "/lustre/scratch/proj/sw/yt/dev/lib/python2.7/site-packages/yt-2.4dev-py2.7-linux-x86_64.egg/yt/funcs .py", line 104, in get_memory_usage return float(os.popen('ps -o rss= -p %d' % pid).read()) / 1024 ValueError: could not convert string to float: PID Uid VmSize Stat Command 1 root 584 S init 2 root SW [migration/0] 3 root SWN [ksoftirqd/0] 4 root SW [migration/1] 5 roo It seems that something went wrong at "get_memory_usage", but I had never had this error before and an interactive job does not get this error either. Sorry the error message is quite messy... Yuan
Hi Yuan, Sorry for the delay in responding to your issue! It seems that fix that was put in place (by me) to get the memory usage isn't working right on Kraken. I am also seeing this behavior. I am looking into this right now. For the time being, you should be ok loading an older yt module, like yt/2.2. Britton On Sat, Feb 25, 2012 at 6:21 PM, Yuan Li <yuan@astro.columbia.edu> wrote:
Hi all,
I am trying to make a simple density projection of my data using yt on kraken. I have done this successfully many times before both on kraken and other machines, but lately I have been getting errors on kraken.
I tried to run it interactively and it worked, but when I submit it as a job, I get this error:
P000 yt : [INFO ] 2012-02-24 03:40:43,722 Created plot collection with default plot-center = [0.50027465 8203125, 0.500335693359375, 0.499969482421875] Traceback (most recent call last): File "/var/spool/alps/8952326/try1.py", line 8, in <module> profile("Feb2012/cluster_64/",imax=20) File "/lustre/scratch/yuan/enzo_yt/cluster256_nog/yuan.py", line 23, in profile File "/lustre/scratch/yuan/enzo_yt/cluster256_nog/yuan.py", line 23, in profile pc.add_projection("Density", 0)
File "/lustre/scratch/proj/sw/yt/dev/lib/python2.7/site-packages/yt-2.4dev-py2.7-linux-x86_64.egg/yt/visua lization/plot_collection.py", line 758, in add_projection
P000 yt : [INFO ] 2012-02-24 03:40:43,919 Starting 'Projecting level 0 / 8 ' **field_parameters) **field_parameters) File
"/lustre/scratch/proj/sw/yt/dev/lib/python2.7/site-packages/yt-2.4dev-py2.7-linux-x86_64. egg/yt/data_objects/data_containers.py", line 1648, in __init__
File "/lustre/scratch/proj/sw/yt/dev/lib/python2.7/site-packages/yt-2.4dev-py2.7-linux-x86_64.egg/yt/data_ objects/data_containers.py", line 309, in _refresh_data
.......
File "/lustre/scratch/proj/sw/yt/dev/lib/python2.7/site-packages/yt-2.4dev-py2.7-linux-x86_64.egg/yt/funcs .py", line 104, in get_memory_usage return float(os.popen('ps -o rss= -p %d' % pid).read()) / 1024 ValueError: could not convert string to float: PID Uid VmSize Stat Command 1 root 584 S init 2 root SW [migration/0] 3 root SWN [ksoftirqd/0] 4 root SW [migration/1] 5 roo
It seems that something went wrong at "get_memory_usage", but I had never had this error before and an interactive job does not get this error either.
Sorry the error message is quite messy...
Yuan _______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
Hi Yuan and others, I was able to verify that the system command yt uses to get memory usage has an slightly non-standard return when run on the Kraken compute nodes. Seeing as how Kraken is a primary target for measuring memory usage, I have tried to implement a fix that will still return the proper number rather than just giving up. I will issue a pull request and try to get this fixed in the code as soon as possible. Britton On Tue, Feb 28, 2012 at 3:41 PM, Britton Smith <brittonsmith@gmail.com>wrote:
Hi Yuan,
Sorry for the delay in responding to your issue! It seems that fix that was put in place (by me) to get the memory usage isn't working right on Kraken. I am also seeing this behavior. I am looking into this right now. For the time being, you should be ok loading an older yt module, like yt/2.2.
Britton
On Sat, Feb 25, 2012 at 6:21 PM, Yuan Li <yuan@astro.columbia.edu> wrote:
Hi all,
I am trying to make a simple density projection of my data using yt on kraken. I have done this successfully many times before both on kraken and other machines, but lately I have been getting errors on kraken.
I tried to run it interactively and it worked, but when I submit it as a job, I get this error:
P000 yt : [INFO ] 2012-02-24 03:40:43,722 Created plot collection with default plot-center = [0.50027465 8203125, 0.500335693359375, 0.499969482421875] Traceback (most recent call last): File "/var/spool/alps/8952326/try1.py", line 8, in <module> profile("Feb2012/cluster_64/",imax=20) File "/lustre/scratch/yuan/enzo_yt/cluster256_nog/yuan.py", line 23, in profile File "/lustre/scratch/yuan/enzo_yt/cluster256_nog/yuan.py", line 23, in profile pc.add_projection("Density", 0)
File "/lustre/scratch/proj/sw/yt/dev/lib/python2.7/site-packages/yt-2.4dev-py2.7-linux-x86_64.egg/yt/visua lization/plot_collection.py", line 758, in add_projection
P000 yt : [INFO ] 2012-02-24 03:40:43,919 Starting 'Projecting level 0 / 8 ' **field_parameters) **field_parameters) File
"/lustre/scratch/proj/sw/yt/dev/lib/python2.7/site-packages/yt-2.4dev-py2.7-linux-x86_64. egg/yt/data_objects/data_containers.py", line 1648, in __init__
File "/lustre/scratch/proj/sw/yt/dev/lib/python2.7/site-packages/yt-2.4dev-py2.7-linux-x86_64.egg/yt/data_ objects/data_containers.py", line 309, in _refresh_data
.......
File "/lustre/scratch/proj/sw/yt/dev/lib/python2.7/site-packages/yt-2.4dev-py2.7-linux-x86_64.egg/yt/funcs .py", line 104, in get_memory_usage return float(os.popen('ps -o rss= -p %d' % pid).read()) / 1024 ValueError: could not convert string to float: PID Uid VmSize Stat Command 1 root 584 S init 2 root SW [migration/0] 3 root SWN [ksoftirqd/0] 4 root SW [migration/1] 5 roo
It seems that something went wrong at "get_memory_usage", but I had never had this error before and an interactive job does not get this error either.
Sorry the error message is quite messy...
Yuan _______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
Hi again everyone, A pull request containing a fix to this bug has been accepted. If after updating anyone encounters errors that trace back to the get_memory_usage function, please let us know. Hari, can you update the yt-dev module on Kraken? Britton On Tue, Feb 28, 2012 at 5:30 PM, Britton Smith <brittonsmith@gmail.com>wrote:
Hi Yuan and others,
I was able to verify that the system command yt uses to get memory usage has an slightly non-standard return when run on the Kraken compute nodes. Seeing as how Kraken is a primary target for measuring memory usage, I have tried to implement a fix that will still return the proper number rather than just giving up. I will issue a pull request and try to get this fixed in the code as soon as possible.
Britton
On Tue, Feb 28, 2012 at 3:41 PM, Britton Smith <brittonsmith@gmail.com>wrote:
Hi Yuan,
Sorry for the delay in responding to your issue! It seems that fix that was put in place (by me) to get the memory usage isn't working right on Kraken. I am also seeing this behavior. I am looking into this right now. For the time being, you should be ok loading an older yt module, like yt/2.2.
Britton
On Sat, Feb 25, 2012 at 6:21 PM, Yuan Li <yuan@astro.columbia.edu> wrote:
Hi all,
I am trying to make a simple density projection of my data using yt on kraken. I have done this successfully many times before both on kraken and other machines, but lately I have been getting errors on kraken.
I tried to run it interactively and it worked, but when I submit it as a job, I get this error:
P000 yt : [INFO ] 2012-02-24 03:40:43,722 Created plot collection with default plot-center = [0.50027465 8203125, 0.500335693359375, 0.499969482421875] Traceback (most recent call last): File "/var/spool/alps/8952326/try1.py", line 8, in <module> profile("Feb2012/cluster_64/",imax=20) File "/lustre/scratch/yuan/enzo_yt/cluster256_nog/yuan.py", line 23, in profile File "/lustre/scratch/yuan/enzo_yt/cluster256_nog/yuan.py", line 23, in profile pc.add_projection("Density", 0)
File "/lustre/scratch/proj/sw/yt/dev/lib/python2.7/site-packages/yt-2.4dev-py2.7-linux-x86_64.egg/yt/visua lization/plot_collection.py", line 758, in add_projection
P000 yt : [INFO ] 2012-02-24 03:40:43,919 Starting 'Projecting level 0 / 8 ' **field_parameters) **field_parameters) File
"/lustre/scratch/proj/sw/yt/dev/lib/python2.7/site-packages/yt-2.4dev-py2.7-linux-x86_64. egg/yt/data_objects/data_containers.py", line 1648, in __init__
File "/lustre/scratch/proj/sw/yt/dev/lib/python2.7/site-packages/yt-2.4dev-py2.7-linux-x86_64.egg/yt/data_ objects/data_containers.py", line 309, in _refresh_data
.......
File "/lustre/scratch/proj/sw/yt/dev/lib/python2.7/site-packages/yt-2.4dev-py2.7-linux-x86_64.egg/yt/funcs .py", line 104, in get_memory_usage return float(os.popen('ps -o rss= -p %d' % pid).read()) / 1024 ValueError: could not convert string to float: PID Uid VmSize Stat Command 1 root 584 S init 2 root SW [migration/0] 3 root SWN [ksoftirqd/0] 4 root SW [migration/1] 5 roo
It seems that something went wrong at "get_memory_usage", but I had never had this error before and an interactive job does not get this error either.
Sorry the error message is quite messy...
Yuan _______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
Hi all, The Kraken yt-dev module just finished updating. Let me know if anyone has any issues with the installation. Also, if the changes did not get updated for some reason. Best regards, Hari On Tue, Feb 28, 2012 at 5:31 PM, Britton Smith <brittonsmith@gmail.com> wrote:
Hi again everyone,
A pull request containing a fix to this bug has been accepted. If after updating anyone encounters errors that trace back to the get_memory_usage function, please let us know.
Hari, can you update the yt-dev module on Kraken?
Britton
On Tue, Feb 28, 2012 at 5:30 PM, Britton Smith <brittonsmith@gmail.com> wrote:
Hi Yuan and others,
I was able to verify that the system command yt uses to get memory usage has an slightly non-standard return when run on the Kraken compute nodes. Seeing as how Kraken is a primary target for measuring memory usage, I have tried to implement a fix that will still return the proper number rather than just giving up. I will issue a pull request and try to get this fixed in the code as soon as possible.
Britton
On Tue, Feb 28, 2012 at 3:41 PM, Britton Smith <brittonsmith@gmail.com> wrote:
Hi Yuan,
Sorry for the delay in responding to your issue! It seems that fix that was put in place (by me) to get the memory usage isn't working right on Kraken. I am also seeing this behavior. I am looking into this right now. For the time being, you should be ok loading an older yt module, like yt/2.2.
Britton
On Sat, Feb 25, 2012 at 6:21 PM, Yuan Li <yuan@astro.columbia.edu> wrote:
Hi all,
I am trying to make a simple density projection of my data using yt on kraken. I have done this successfully many times before both on kraken and other machines, but lately I have been getting errors on kraken.
I tried to run it interactively and it worked, but when I submit it as a job, I get this error:
P000 yt : [INFO ] 2012-02-24 03:40:43,722 Created plot collection with default plot-center = [0.50027465 8203125, 0.500335693359375, 0.499969482421875] Traceback (most recent call last): File "/var/spool/alps/8952326/try1.py", line 8, in <module> profile("Feb2012/cluster_64/",imax=20) File "/lustre/scratch/yuan/enzo_yt/cluster256_nog/yuan.py", line 23, in profile File "/lustre/scratch/yuan/enzo_yt/cluster256_nog/yuan.py", line 23, in profile pc.add_projection("Density", 0)
File "/lustre/scratch/proj/sw/yt/dev/lib/python2.7/site-packages/yt-2.4dev-py2.7-linux-x86_64.egg/yt/visua lization/plot_collection.py", line 758, in add_projection
P000 yt : [INFO ] 2012-02-24 03:40:43,919 Starting 'Projecting level 0 / 8 ' **field_parameters) **field_parameters) File
"/lustre/scratch/proj/sw/yt/dev/lib/python2.7/site-packages/yt-2.4dev-py2.7-linux-x86_64. egg/yt/data_objects/data_containers.py", line 1648, in __init__
File "/lustre/scratch/proj/sw/yt/dev/lib/python2.7/site-packages/yt-2.4dev-py2.7-linux-x86_64.egg/yt/data_ objects/data_containers.py", line 309, in _refresh_data
.......
File "/lustre/scratch/proj/sw/yt/dev/lib/python2.7/site-packages/yt-2.4dev-py2.7-linux-x86_64.egg/yt/funcs .py", line 104, in get_memory_usage return float(os.popen('ps -o rss= -p %d' % pid).read()) / 1024 ValueError: could not convert string to float: PID Uid VmSize Stat Command 1 root 584 S init 2 root SW [migration/0] 3 root SWN [ksoftirqd/0] 4 root SW [migration/1] 5 roo
It seems that something went wrong at "get_memory_usage", but I had never had this error before and an interactive job does not get this error either.
Sorry the error message is quite messy...
Yuan _______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
participants (3)
-
Britton Smith -
Harinarayan Krishnan -
Yuan Li