Hi all, I'm trying to run yt on a login node on kraken. All I'm doing is invoking python from the command line and importing yt. However, python hangs on 'from yt.mods import *'. The python interpreter also takes a very long time (~ a minute or so) to start from the command line. This happens using both the yt/dev and yt/2.3 module. Anyone have any ideas? Nathan Goldbaum Graduate Student Astronomy & Astrophysics, UCSC goldbaum@ucolick.org http://www.ucolick.org/~goldbaum
Hi Nathan, It's most likely not hanging, but working on the import. The filesystem on Kraken can be incredibly slow at times. If you're only waiting a minute or so, you will probably need to give it a bit longer. Britton On Wed, Feb 22, 2012 at 5:15 PM, Nathan Goldbaum <goldbaum@ucolick.org>wrote:
Hi all,
I'm trying to run yt on a login node on kraken. All I'm doing is invoking python from the command line and importing yt. However, python hangs on 'from yt.mods import *'.
The python interpreter also takes a very long time (~ a minute or so) to start from the command line.
This happens using both the yt/dev and yt/2.3 module.
Anyone have any ideas?
Nathan Goldbaum Graduate Student Astronomy & Astrophysics, UCSC goldbaum@ucolick.org http://www.ucolick.org/~goldbaum
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Hi Britton, Thanks for the suggestion. I've been waiting for more than 10 minutes now and it still hasn't finished the import - does that seem excessive? Nathan Goldbaum Graduate Student Astronomy & Astrophysics, UCSC goldbaum@ucolick.org http://www.ucolick.org/~goldbaum On Feb 22, 2012, at 2:19 PM, Britton Smith wrote:
Hi Nathan,
It's most likely not hanging, but working on the import. The filesystem on Kraken can be incredibly slow at times. If you're only waiting a minute or so, you will probably need to give it a bit longer.
Britton
On Wed, Feb 22, 2012 at 5:15 PM, Nathan Goldbaum <goldbaum@ucolick.org> wrote: Hi all,
I'm trying to run yt on a login node on kraken. All I'm doing is invoking python from the command line and importing yt. However, python hangs on 'from yt.mods import *'.
The python interpreter also takes a very long time (~ a minute or so) to start from the command line.
This happens using both the yt/dev and yt/2.3 module.
Anyone have any ideas?
Nathan Goldbaum Graduate Student Astronomy & Astrophysics, UCSC goldbaum@ucolick.org http://www.ucolick.org/~goldbaum
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Hi Nathan, That's on the high side a little, but, sadly, not the maximum I've ever waited. Britton On Wed, Feb 22, 2012 at 5:33 PM, Nathan Goldbaum <goldbaum@ucolick.org>wrote:
Hi Britton,
Thanks for the suggestion. I've been waiting for more than 10 minutes now and it still hasn't finished the import - does that seem excessive?
Nathan Goldbaum Graduate Student Astronomy & Astrophysics, UCSC goldbaum@ucolick.org http://www.ucolick.org/~goldbaum
On Feb 22, 2012, at 2:19 PM, Britton Smith wrote:
Hi Nathan,
It's most likely not hanging, but working on the import. The filesystem on Kraken can be incredibly slow at times. If you're only waiting a minute or so, you will probably need to give it a bit longer.
Britton
On Wed, Feb 22, 2012 at 5:15 PM, Nathan Goldbaum <goldbaum@ucolick.org>wrote:
Hi all,
I'm trying to run yt on a login node on kraken. All I'm doing is invoking python from the command line and importing yt. However, python hangs on 'from yt.mods import *'.
The python interpreter also takes a very long time (~ a minute or so) to start from the command line.
This happens using both the yt/dev and yt/2.3 module.
Anyone have any ideas?
Nathan Goldbaum Graduate Student Astronomy & Astrophysics, UCSC goldbaum@ucolick.org http://www.ucolick.org/~goldbaum
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I would recommend if possible getting an interactive node to try yt on. I've seen many users abuse the login node of Kraken, running multiple jobs, and sometimes it's multiple users at the same time that slows the node down. Have you tried another login node of Kraken, since there's 11 to choose from. If I do >top and see many jobs running I usually just switch, ssh -Y krakenpf1 you can do this all the way to krakenpf11 From G.S. On Wed, Feb 22, 2012 at 2:35 PM, Britton Smith <brittonsmith@gmail.com>wrote:
Hi Nathan,
That's on the high side a little, but, sadly, not the maximum I've ever waited.
Britton
On Wed, Feb 22, 2012 at 5:33 PM, Nathan Goldbaum <goldbaum@ucolick.org>wrote:
Hi Britton,
Thanks for the suggestion. I've been waiting for more than 10 minutes now and it still hasn't finished the import - does that seem excessive?
Nathan Goldbaum Graduate Student Astronomy & Astrophysics, UCSC goldbaum@ucolick.org http://www.ucolick.org/~goldbaum
On Feb 22, 2012, at 2:19 PM, Britton Smith wrote:
Hi Nathan,
It's most likely not hanging, but working on the import. The filesystem on Kraken can be incredibly slow at times. If you're only waiting a minute or so, you will probably need to give it a bit longer.
Britton
On Wed, Feb 22, 2012 at 5:15 PM, Nathan Goldbaum <goldbaum@ucolick.org>wrote:
Hi all,
I'm trying to run yt on a login node on kraken. All I'm doing is invoking python from the command line and importing yt. However, python hangs on 'from yt.mods import *'.
The python interpreter also takes a very long time (~ a minute or so) to start from the command line.
This happens using both the yt/dev and yt/2.3 module.
Anyone have any ideas?
Nathan Goldbaum Graduate Student Astronomy & Astrophysics, UCSC goldbaum@ucolick.org http://www.ucolick.org/~goldbaum
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Hi Geoffrey, I ended up starting an interactive job on a compute node. The import still took about 10 minutes. It finally did finish importing though. Nathan Goldbaum Graduate Student Astronomy & Astrophysics, UCSC goldbaum@ucolick.org http://www.ucolick.org/~goldbaum On Feb 22, 2012, at 2:45 PM, Geoffrey So wrote:
I would recommend if possible getting an interactive node to try yt on. I've seen many users abuse the login node of Kraken, running multiple jobs, and sometimes it's multiple users at the same time that slows the node down. Have you tried another login node of Kraken, since there's 11 to choose from.
If I do >top and see many jobs running I usually just switch,
ssh -Y krakenpf1
you can do this all the way to krakenpf11
From G.S.
On Wed, Feb 22, 2012 at 2:35 PM, Britton Smith <brittonsmith@gmail.com> wrote: Hi Nathan,
That's on the high side a little, but, sadly, not the maximum I've ever waited.
Britton
On Wed, Feb 22, 2012 at 5:33 PM, Nathan Goldbaum <goldbaum@ucolick.org> wrote: Hi Britton,
Thanks for the suggestion. I've been waiting for more than 10 minutes now and it still hasn't finished the import - does that seem excessive?
Nathan Goldbaum Graduate Student Astronomy & Astrophysics, UCSC goldbaum@ucolick.org http://www.ucolick.org/~goldbaum
On Feb 22, 2012, at 2:19 PM, Britton Smith wrote:
Hi Nathan,
It's most likely not hanging, but working on the import. The filesystem on Kraken can be incredibly slow at times. If you're only waiting a minute or so, you will probably need to give it a bit longer.
Britton
On Wed, Feb 22, 2012 at 5:15 PM, Nathan Goldbaum <goldbaum@ucolick.org> wrote: Hi all,
I'm trying to run yt on a login node on kraken. All I'm doing is invoking python from the command line and importing yt. However, python hangs on 'from yt.mods import *'.
The python interpreter also takes a very long time (~ a minute or so) to start from the command line.
This happens using both the yt/dev and yt/2.3 module.
Anyone have any ideas?
Nathan Goldbaum Graduate Student Astronomy & Astrophysics, UCSC goldbaum@ucolick.org http://www.ucolick.org/~goldbaum
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Yeah interactive is the way to go if you don't want to fight over system resources or hog the login node, problem is sometimes it takes a long time for interactive session to even start. Glad it worked for you :-) From G.S. On Wed, Feb 22, 2012 at 2:47 PM, Nathan Goldbaum <goldbaum@ucolick.org>wrote:
Hi Geoffrey,
I ended up starting an interactive job on a compute node. The import still took about 10 minutes. It finally did finish importing though.
Nathan Goldbaum Graduate Student Astronomy & Astrophysics, UCSC goldbaum@ucolick.org http://www.ucolick.org/~goldbaum
On Feb 22, 2012, at 2:45 PM, Geoffrey So wrote:
I would recommend if possible getting an interactive node to try yt on. I've seen many users abuse the login node of Kraken, running multiple jobs, and sometimes it's multiple users at the same time that slows the node down. Have you tried another login node of Kraken, since there's 11 to choose from.
If I do >top and see many jobs running I usually just switch,
ssh -Y krakenpf1
you can do this all the way to krakenpf11
From G.S.
On Wed, Feb 22, 2012 at 2:35 PM, Britton Smith <brittonsmith@gmail.com>wrote:
Hi Nathan,
That's on the high side a little, but, sadly, not the maximum I've ever waited.
Britton
On Wed, Feb 22, 2012 at 5:33 PM, Nathan Goldbaum <goldbaum@ucolick.org>wrote:
Hi Britton,
Thanks for the suggestion. I've been waiting for more than 10 minutes now and it still hasn't finished the import - does that seem excessive?
Nathan Goldbaum Graduate Student Astronomy & Astrophysics, UCSC goldbaum@ucolick.org http://www.ucolick.org/~goldbaum
On Feb 22, 2012, at 2:19 PM, Britton Smith wrote:
Hi Nathan,
It's most likely not hanging, but working on the import. The filesystem on Kraken can be incredibly slow at times. If you're only waiting a minute or so, you will probably need to give it a bit longer.
Britton
On Wed, Feb 22, 2012 at 5:15 PM, Nathan Goldbaum <goldbaum@ucolick.org>wrote:
Hi all,
I'm trying to run yt on a login node on kraken. All I'm doing is invoking python from the command line and importing yt. However, python hangs on 'from yt.mods import *'.
The python interpreter also takes a very long time (~ a minute or so) to start from the command line.
This happens using both the yt/dev and yt/2.3 module.
Anyone have any ideas?
Nathan Goldbaum Graduate Student Astronomy & Astrophysics, UCSC goldbaum@ucolick.org http://www.ucolick.org/~goldbaum
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This problem is often independent of the load on whatever node you're on. It's more affected by the load being placed on the filesystem, which I don't think there's a way to measure. When the lustre system is being hit hard, it won't matter if you're on a login node or a compute node. On Feb 22, 2012 5:53 PM, "Geoffrey So" <gsiisg@gmail.com> wrote:
Yeah interactive is the way to go if you don't want to fight over system resources or hog the login node, problem is sometimes it takes a long time for interactive session to even start.
Glad it worked for you :-)
From G.S.
On Wed, Feb 22, 2012 at 2:47 PM, Nathan Goldbaum <goldbaum@ucolick.org>wrote:
Hi Geoffrey,
I ended up starting an interactive job on a compute node. The import still took about 10 minutes. It finally did finish importing though.
Nathan Goldbaum Graduate Student Astronomy & Astrophysics, UCSC goldbaum@ucolick.org http://www.ucolick.org/~goldbaum
On Feb 22, 2012, at 2:45 PM, Geoffrey So wrote:
I would recommend if possible getting an interactive node to try yt on. I've seen many users abuse the login node of Kraken, running multiple jobs, and sometimes it's multiple users at the same time that slows the node down. Have you tried another login node of Kraken, since there's 11 to choose from.
If I do >top and see many jobs running I usually just switch,
ssh -Y krakenpf1
you can do this all the way to krakenpf11
From G.S.
On Wed, Feb 22, 2012 at 2:35 PM, Britton Smith <brittonsmith@gmail.com>wrote:
Hi Nathan,
That's on the high side a little, but, sadly, not the maximum I've ever waited.
Britton
On Wed, Feb 22, 2012 at 5:33 PM, Nathan Goldbaum <goldbaum@ucolick.org>wrote:
Hi Britton,
Thanks for the suggestion. I've been waiting for more than 10 minutes now and it still hasn't finished the import - does that seem excessive?
Nathan Goldbaum Graduate Student Astronomy & Astrophysics, UCSC goldbaum@ucolick.org http://www.ucolick.org/~goldbaum
On Feb 22, 2012, at 2:19 PM, Britton Smith wrote:
Hi Nathan,
It's most likely not hanging, but working on the import. The filesystem on Kraken can be incredibly slow at times. If you're only waiting a minute or so, you will probably need to give it a bit longer.
Britton
On Wed, Feb 22, 2012 at 5:15 PM, Nathan Goldbaum <goldbaum@ucolick.org>wrote:
Hi all,
I'm trying to run yt on a login node on kraken. All I'm doing is invoking python from the command line and importing yt. However, python hangs on 'from yt.mods import *'.
The python interpreter also takes a very long time (~ a minute or so) to start from the command line.
This happens using both the yt/dev and yt/2.3 module.
Anyone have any ideas?
Nathan Goldbaum Graduate Student Astronomy & Astrophysics, UCSC goldbaum@ucolick.org http://www.ucolick.org/~goldbaum
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I ended up starting an interactive job on a compute node. The import still took about 10 minutes. It finally did finish importing though.
It doesn't surprise me that it still took that long even on an interactive node. The problem isn't the node but the disk, and 100% of the disks on Kraken are 100% terrible and getting worse. I almost always shuffle my stuff to Nautilus, if you have an account there. Using hpss and/or htar to transfer files between the two is really fast (limited only by Kraken's disk) you can get dozens of Gb in minutes. (If they're small sets, you can use the home disk to transfer.)
Nathan Goldbaum Graduate Student Astronomy & Astrophysics, UCSC goldbaum@ucolick.org http://www.ucolick.org/~goldbaum
On Feb 22, 2012, at 2:45 PM, Geoffrey So wrote:
I would recommend if possible getting an interactive node to try yt on. I've seen many users abuse the login node of Kraken, running multiple jobs, and sometimes it's multiple users at the same time that slows the node down. Have you tried another login node of Kraken, since there's 11 to choose from.
If I do >top and see many jobs running I usually just switch,
ssh -Y krakenpf1
you can do this all the way to krakenpf11
From G.S.
On Wed, Feb 22, 2012 at 2:35 PM, Britton Smith <brittonsmith@gmail.com> wrote:
Hi Nathan,
That's on the high side a little, but, sadly, not the maximum I've ever waited.
Britton
On Wed, Feb 22, 2012 at 5:33 PM, Nathan Goldbaum <goldbaum@ucolick.org> wrote:
Hi Britton,
Thanks for the suggestion. I've been waiting for more than 10 minutes now and it still hasn't finished the import - does that seem excessive?
Nathan Goldbaum Graduate Student Astronomy & Astrophysics, UCSC goldbaum@ucolick.org http://www.ucolick.org/~goldbaum
On Feb 22, 2012, at 2:19 PM, Britton Smith wrote:
Hi Nathan,
It's most likely not hanging, but working on the import. The filesystem on Kraken can be incredibly slow at times. If you're only waiting a minute or so, you will probably need to give it a bit longer.
Britton
On Wed, Feb 22, 2012 at 5:15 PM, Nathan Goldbaum <goldbaum@ucolick.org> wrote:
Hi all,
I'm trying to run yt on a login node on kraken. All I'm doing is invoking python from the command line and importing yt. However, python hangs on 'from yt.mods import *'.
The python interpreter also takes a very long time (~ a minute or so) to start from the command line.
This happens using both the yt/dev and yt/2.3 module.
Anyone have any ideas?
Nathan Goldbaum Graduate Student Astronomy & Astrophysics, UCSC goldbaum@ucolick.org http://www.ucolick.org/~goldbaum
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-- Sent from my computer.
Nathan, I was using Kraken this afternoon as well, and it was one of the longest waits I've had in terms of system delays. So it wasn't just you--we were all suffering from it. On 02/22/2012 06:38 PM, David Collins wrote:
I ended up starting an interactive job on a compute node. The import still took about 10 minutes. It finally did finish importing though. It doesn't surprise me that it still took that long even on an interactive node. The problem isn't the node but the disk, and 100% of the disks on Kraken are 100% terrible and getting worse.
I almost always shuffle my stuff to Nautilus, if you have an account there. Using hpss and/or htar to transfer files between the two is really fast (limited only by Kraken's disk) you can get dozens of Gb in minutes. (If they're small sets, you can use the home disk to transfer.)
Nathan Goldbaum Graduate Student Astronomy & Astrophysics, UCSC goldbaum@ucolick.org http://www.ucolick.org/~goldbaum
On Feb 22, 2012, at 2:45 PM, Geoffrey So wrote:
I would recommend if possible getting an interactive node to try yt on. I've seen many users abuse the login node of Kraken, running multiple jobs, and sometimes it's multiple users at the same time that slows the node down. Have you tried another login node of Kraken, since there's 11 to choose from.
If I do >top and see many jobs running I usually just switch,
ssh -Y krakenpf1
you can do this all the way to krakenpf11
From G.S.
On Wed, Feb 22, 2012 at 2:35 PM, Britton Smith <brittonsmith@gmail.com> wrote:
Hi Nathan,
That's on the high side a little, but, sadly, not the maximum I've ever waited.
Britton
On Wed, Feb 22, 2012 at 5:33 PM, Nathan Goldbaum <goldbaum@ucolick.org> wrote:
Hi Britton,
Thanks for the suggestion. I've been waiting for more than 10 minutes now and it still hasn't finished the import - does that seem excessive?
Nathan Goldbaum Graduate Student Astronomy & Astrophysics, UCSC goldbaum@ucolick.org http://www.ucolick.org/~goldbaum
On Feb 22, 2012, at 2:19 PM, Britton Smith wrote:
Hi Nathan,
It's most likely not hanging, but working on the import. The filesystem on Kraken can be incredibly slow at times. If you're only waiting a minute or so, you will probably need to give it a bit longer.
Britton
On Wed, Feb 22, 2012 at 5:15 PM, Nathan Goldbaum <goldbaum@ucolick.org> wrote:
Hi all,
I'm trying to run yt on a login node on kraken. All I'm doing is invoking python from the command line and importing yt. However, python hangs on 'from yt.mods import *'.
The python interpreter also takes a very long time (~ a minute or so) to start from the command line.
This happens using both the yt/dev and yt/2.3 module.
Anyone have any ideas?
Nathan Goldbaum Graduate Student Astronomy & Astrophysics, UCSC goldbaum@ucolick.org http://www.ucolick.org/~goldbaum
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-- Cameron Hummels PhD Candidate, Astronomy Department of Columbia University Public Outreach Director, Astronomy Department of Columbia University NASA IYA New York State Student Ambassador http://outreach.astro.columbia.edu PGP: 0x06F886E3
Both the python interpreter and all modules associated with the "module load yt/dev" on kraken live on a luster filesytem. In general I've found the kraken luster system to have reasonable bandwidth but high to intermittently *extremely high* latency for accessing files. The yt import accesses lots of files and consequently the import from this yt installation ranges anywhere from annoyingly slow to unusable. Compute nodes or lightly loaded head nodes are sometimes better, sometimes not it seems. I've install my own build in my home directory on that machine just because of this. Because the home directory is not luster, an install in this location can load up normally. I have not had the yt slow-to-start problem since I did this. The quota on the kraken home directory is too small for the yt installer script to download the whole kitchen sink. However I did manage to install the hdf5, h5py, numpy, scipy, matplotlib, setuptools, cython and pip packages manually for the kraken system python 2.6 and the latest gcc modules. That did fit in the alloted home space and did finally get all the dependencies yt needs working for me. On Wed, 22 Feb 2012, Britton Smith wrote:
Hi Nathan,
It's most likely not hanging, but working on the import. The filesystem on Kraken can be incredibly slow at times. If you're only waiting a minute or so, you will probably need to give it a bit longer.
Britton
On Wed, Feb 22, 2012 at 5:15 PM, Nathan Goldbaum <goldbaum@ucolick.org> wrote: Hi all,
I'm trying to run yt on a login node on kraken. All I'm doing is invoking python from the command line and importing yt. However, python hangs on 'from yt.mods import *'.
The python interpreter also takes a very long time (~ a minute or so) to start from the command line.
This happens using both the yt/dev and yt/2.3 module.
Anyone have any ideas?
Nathan Goldbaum Graduate Student Astronomy & Astrophysics, UCSC goldbaum@ucolick.org http://www.ucolick.org/~goldbaum
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Would it be impossible to install the yt module on an NFS filesystem? I gather that Hari Krishnan reads this user list, maybe he can weigh in on some best practices for using the yt module on Kraken. Nathan Goldbaum Graduate Student Astronomy & Astrophysics, UCSC goldbaum@ucolick.org http://www.ucolick.org/~goldbaum On Feb 22, 2012, at 4:40 PM, Andrew Cunningham wrote:
Both the python interpreter and all modules associated with the "module load yt/dev" on kraken live on a luster filesytem. In general I've found the kraken luster system to have reasonable bandwidth but high to intermittently *extremely high* latency for accessing files. The yt import accesses lots of files and consequently the import from this yt installation ranges anywhere from annoyingly slow to unusable. Compute nodes or lightly loaded head nodes are sometimes better, sometimes not it seems.
I've install my own build in my home directory on that machine just because of this. Because the home directory is not luster, an install in this location can load up normally. I have not had the yt slow-to-start problem since I did this.
The quota on the kraken home directory is too small for the yt installer script to download the whole kitchen sink. However I did manage to install the hdf5, h5py, numpy, scipy, matplotlib, setuptools, cython and pip packages manually for the kraken system python 2.6 and the latest gcc modules. That did fit in the alloted home space and did finally get all the dependencies yt needs working for me.
On Wed, 22 Feb 2012, Britton Smith wrote:
Hi Nathan, It's most likely not hanging, but working on the import. The filesystem on Kraken can be incredibly slow at times. If you're only waiting a minute or so, you will probably need to give it a bit longer. Britton On Wed, Feb 22, 2012 at 5:15 PM, Nathan Goldbaum <goldbaum@ucolick.org> wrote: Hi all,
I'm trying to run yt on a login node on kraken. All I'm doing is invoking python from the command line and importing yt. However, python hangs on 'from yt.mods import *'.
The python interpreter also takes a very long time (~ a minute or so) to start from the command line.
This happens using both the yt/dev and yt/2.3 module.
Anyone have any ideas?
Nathan Goldbaum Graduate Student Astronomy & Astrophysics, UCSC goldbaum@ucolick.org http://www.ucolick.org/~goldbaum
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Hi Nathan,
Would it be impossible to install the yt module on an NFS filesystem? I gather that Hari Krishnan reads this user list, maybe he can weigh in on some best practices for using the yt module on Kraken.
It is possible to install the yt on NFS. But you can not access it from compute nodes. You can only use it on login nodes. Pragnesh On Feb 22, 2012, at 4:40 PM, Andrew Cunningham wrote:
Both the python interpreter and all modules associated with the "module load yt/dev" on kraken live on a luster filesytem. In general I've found the kraken luster system to have reasonable bandwidth but high to intermittently *extremely high* latency for accessing files. The yt import accesses lots of files and consequently the import from this yt installation ranges anywhere from annoyingly slow to unusable. Compute nodes or lightly loaded head nodes are sometimes better, sometimes not it seems.
I've install my own build in my home directory on that machine just because of this. Because the home directory is not luster, an install in this location can load up normally. I have not had the yt slow-to-start problem since I did this.
The quota on the kraken home directory is too small for the yt installer script to download the whole kitchen sink. However I did manage to install the hdf5, h5py, numpy, scipy, matplotlib, setuptools, cython and pip packages manually for the kraken system python 2.6 and the latest gcc modules. That did fit in the alloted home space and did finally get all the dependencies yt needs working for me.
On Wed, 22 Feb 2012, Britton Smith wrote:
Hi Nathan, It's most likely not hanging, but working on the import. The filesystem on Kraken can be incredibly slow at times. If you're only waiting a minute or so, you will probably need to give it a bit longer. Britton On Wed, Feb 22, 2012 at 5:15 PM, Nathan Goldbaum <goldbaum@ucolick.org> wrote: Hi all,
I'm trying to run yt on a login node on kraken. All I'm doing is invoking python from the command line and importing yt. However, python hangs on 'from yt.mods import *'.
The python interpreter also takes a very long time (~ a minute or so) to start from the command line.
This happens using both the yt/dev and yt/2.3 module.
Anyone have any ideas?
Nathan Goldbaum Graduate Student Astronomy & Astrophysics, UCSC goldbaum@ucolick.org http://www.ucolick.org/~goldbaum
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I can use a yt build that lives in my home directory to process data that lives on scratch from the compute nodes using an interactive qsub -I job. On an non-interactice job I do need to take care that the matplotlib backend is set to something that doesn't require X. I don't know how what type of filesystem $HOME is in terms of the mounting, but the situation would be substantially improved if the builds used by "module load yt/dev" lived on a filesystem that is more like /nics/d/home and less like /lustre/scratch.
It is possible to install the yt on NFS. But you can not access it from compute nodes. You can only use it on login nodes.
Pragnesh
Hi all, On Kraken, I always build Yt on the /sw/xt filesystem which is accessible to the login nodes before I copy the resulting installation to Lustre. So, I can provide a module load command that points to the version I create on there. For example, loading would be as simple as: "module load yt/2.3-login-node" I have two concerns about this: First, users would have to be aware that the login-node variants of Yt will not be available on compute nodes. Also, the login versions will not have access to MPI. Second and more importantly, login nodes are typically not meant to be used as a place where one performs heavy computation and analysis. They are primarily meant to be responsive and serve as a gateway to the compute nodes. I am all for trying to enable faster launches of Yt, but my concern is that enabling this would open up the possibility of someone launching large jobs and effectively rendering that login node useless for anyone else. With a limited number of login nodes on Kraken, crippling any one of them has the potential of making a lot other users unhappy. I guess since users can potentially run yt on the login nodes right now from their own local installation or the one available on Lustre, this makes the my concern moot. I guess I can enable loading yt using the xt filesystem and see if Kraken's administrators send me a nasty email if someone abuses this feature :) Best regards, Hari On Wed, Feb 22, 2012 at 5:13 PM, Patel, Pragneshkumar B <pragnesh@utk.edu> wrote:
Hi Nathan,
Would it be impossible to install the yt module on an NFS filesystem? I gather that Hari Krishnan reads this user list, maybe he can weigh in on some best practices for using the yt module on Kraken.
It is possible to install the yt on NFS. But you can not access it from compute nodes. You can only use it on login nodes.
Pragnesh
On Feb 22, 2012, at 4:40 PM, Andrew Cunningham wrote:
Both the python interpreter and all modules associated with the "module load yt/dev" on kraken live on a luster filesytem. In general I've found the kraken luster system to have reasonable bandwidth but high to intermittently *extremely high* latency for accessing files. The yt import accesses lots of files and consequently the import from this yt installation ranges anywhere from annoyingly slow to unusable. Compute nodes or lightly loaded head nodes are sometimes better, sometimes not it seems.
I've install my own build in my home directory on that machine just because of this. Because the home directory is not luster, an install in this location can load up normally. I have not had the yt slow-to-start problem since I did this.
The quota on the kraken home directory is too small for the yt installer script to download the whole kitchen sink. However I did manage to install the hdf5, h5py, numpy, scipy, matplotlib, setuptools, cython and pip packages manually for the kraken system python 2.6 and the latest gcc modules. That did fit in the alloted home space and did finally get all the dependencies yt needs working for me.
On Wed, 22 Feb 2012, Britton Smith wrote:
Hi Nathan, It's most likely not hanging, but working on the import. The filesystem on Kraken can be incredibly slow at times. If you're only waiting a minute or so, you will probably need to give it a bit longer. Britton On Wed, Feb 22, 2012 at 5:15 PM, Nathan Goldbaum <goldbaum@ucolick.org> wrote: Hi all,
I'm trying to run yt on a login node on kraken. All I'm doing is invoking python from the command line and importing yt. However, python hangs on 'from yt.mods import *'.
The python interpreter also takes a very long time (~ a minute or so) to start from the command line.
This happens using both the yt/dev and yt/2.3 module.
Anyone have any ideas?
Nathan Goldbaum Graduate Student Astronomy & Astrophysics, UCSC goldbaum@ucolick.org http://www.ucolick.org/~goldbaum
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Hi all, On Kraken, I have enabled the ability to load yt on login. The command is: "module swap PrgEnv-pgi PrgEnv-gnu" "module load yt/2.3-local" or "module load yt/dev-local" I stress again, please use it only for small tasks and tests. Running large jobs on login nodes can/will cripple a very limited resource. Also, the admins may boot you off the system if you take over the machine. Let me know if you any question, concerns, or if something is not working properly. Best regards, Hari On Wed, Feb 22, 2012 at 7:20 PM, Harinarayan Krishnan <hkrishnan@lbl.gov> wrote:
Hi all,
On Kraken, I always build Yt on the /sw/xt filesystem which is accessible to the login nodes before I copy the resulting installation to Lustre. So, I can provide a module load command that points to the version I create on there.
For example, loading would be as simple as: "module load yt/2.3-login-node"
I have two concerns about this:
First, users would have to be aware that the login-node variants of Yt will not be available on compute nodes. Also, the login versions will not have access to MPI.
Second and more importantly, login nodes are typically not meant to be used as a place where one performs heavy computation and analysis. They are primarily meant to be responsive and serve as a gateway to the compute nodes.
I am all for trying to enable faster launches of Yt, but my concern is that enabling this would open up the possibility of someone launching large jobs and effectively rendering that login node useless for anyone else. With a limited number of login nodes on Kraken, crippling any one of them has the potential of making a lot other users unhappy.
I guess since users can potentially run yt on the login nodes right now from their own local installation or the one available on Lustre, this makes the my concern moot. I guess I can enable loading yt using the xt filesystem and see if Kraken's administrators send me a nasty email if someone abuses this feature :)
Best regards, Hari
On Wed, Feb 22, 2012 at 5:13 PM, Patel, Pragneshkumar B <pragnesh@utk.edu> wrote:
Hi Nathan,
Would it be impossible to install the yt module on an NFS filesystem? I gather that Hari Krishnan reads this user list, maybe he can weigh in on some best practices for using the yt module on Kraken.
It is possible to install the yt on NFS. But you can not access it from compute nodes. You can only use it on login nodes.
Pragnesh
On Feb 22, 2012, at 4:40 PM, Andrew Cunningham wrote:
Both the python interpreter and all modules associated with the "module load yt/dev" on kraken live on a luster filesytem. In general I've found the kraken luster system to have reasonable bandwidth but high to intermittently *extremely high* latency for accessing files. The yt import accesses lots of files and consequently the import from this yt installation ranges anywhere from annoyingly slow to unusable. Compute nodes or lightly loaded head nodes are sometimes better, sometimes not it seems.
I've install my own build in my home directory on that machine just because of this. Because the home directory is not luster, an install in this location can load up normally. I have not had the yt slow-to-start problem since I did this.
The quota on the kraken home directory is too small for the yt installer script to download the whole kitchen sink. However I did manage to install the hdf5, h5py, numpy, scipy, matplotlib, setuptools, cython and pip packages manually for the kraken system python 2.6 and the latest gcc modules. That did fit in the alloted home space and did finally get all the dependencies yt needs working for me.
On Wed, 22 Feb 2012, Britton Smith wrote:
Hi Nathan, It's most likely not hanging, but working on the import. The filesystem on Kraken can be incredibly slow at times. If you're only waiting a minute or so, you will probably need to give it a bit longer. Britton On Wed, Feb 22, 2012 at 5:15 PM, Nathan Goldbaum <goldbaum@ucolick.org> wrote: Hi all,
I'm trying to run yt on a login node on kraken. All I'm doing is invoking python from the command line and importing yt. However, python hangs on 'from yt.mods import *'.
The python interpreter also takes a very long time (~ a minute or so) to start from the command line.
This happens using both the yt/dev and yt/2.3 module.
Anyone have any ideas?
Nathan Goldbaum Graduate Student Astronomy & Astrophysics, UCSC goldbaum@ucolick.org http://www.ucolick.org/~goldbaum
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participants (8)
-
Andrew Cunningham -
Britton Smith -
Cameron Hummels -
David Collins -
Geoffrey So -
Harinarayan Krishnan -
Nathan Goldbaum -
Patel, Pragneshkumar B