[Rocks-Discuss] Sharing Apps Directory
David Hoskinson
folder we have put various apps that we need to do our processing. I don¹t
see on the compute nodes however a mount for this directory. I do see how
home is being mounted from the frontend to each compute node. Could someone
let me know how to ³export² the apps directory so its in the same place on
each compute node. I also see in the exports file under etc that export is
being nfs shared but when I tried mounting frontend.local:/export/apps it
didn¹t seem to work.
Thanks
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Paul Kopec
frontend and nfs mounted on all the compute nodes under the same name.
______________________________________________________
Paul Kopec
Project Manager
University of Michigan
Dept. of Human Genetics
1241 E. Catherine Street
5928 Buhl Building
Ann Arbor, MI 48109-0618
734-763-5411
pko...@umich.edu
David Hoskinson
hidden folders until you actually navigate to the under nfs got me. I had
looked in share but didn't cd to apps. Thanks
Paul Kopec
The same will be for all your users /home/<user>.
You may do a ls on /home and only see your
current logon, no other users. Scares some people. :)
You can always go to the hard path to see what is out there.
e.g. /state/partition1/home, /state/partititon/apps, etc...
Bart Brashers
To make the contents visible, make the line in /etc/auto.master look like this:
/share /etc/auto.share --ghost --timeout=1200
Bart Brashers
> -----Original Message-----
> From: npaci-rocks-dis...@sdsc.edu [mailto:npaci-rocks-dis...@sdsc.edu] On
> Behalf Of David Hoskinson
> Sent: Wednesday, October 01, 2008 7:53 AM
> To: Discussion of Rocks Clusters
> Subject: Re: [Rocks-Discuss] Sharing Apps Directory
>
> >From what I am seeing that is the default... Thanks for the path. Stupid
> hidden folders until you actually navigate to the under nfs got me. I had
> looked in share but didn't cd to apps. Thanks
>
>
> On 10/1/08 9:03 AM, "Paul Kopec" <pko...@umich.edu> wrote:
>
> > The default setup is that /share/apps is on the
> > frontend and nfs mounted on all the compute nodes under the same name.
> >
> > At 09:54 AM 10/1/2008, you wrote:
> >> On the frontend under the export directory is a folder called apps. In this
> >> folder we have put various apps that we need to do our processing. I don¹t
> >> see on the compute nodes however a mount for this directory. I do see how
> >> home is being mounted from the frontend to each compute node. Could someone
> >> let me know how to ³export² the apps directory so its in the same place on
> >> each compute node. I also see in the exports file under etc that export is
> >> being nfs shared but when I tried mounting frontend.local:/export/apps it
> >> didn¹t seem to work.
This message contains information that may be confidential, privileged or otherwise protected by law from disclosure. It is intended for the exclusive use of the Addressee(s). Unless you are the addressee or authorized agent of the addressee, you may not review, copy, distribute or disclose to anyone the message or any information contained within. If you have received this message in error, please contact the sender by electronic reply to em...@environcorp.com and immediately delete all copies of the message.
David Hoskinson
to something my users know to keep them from getting confused.
Adrian Robles Ramirez
Hi everybody,
i didn't see the complete answer so i still having a doubt. In my case in the frontend i can see that 'export' is a autofs directory and i also see the 'share' folder. On the node side i just see the the 'share' folder and i can access it and see that exists the 'apps' folder. Into that folder there are all the apps i have installed. However on the frontend side i see the same folder structure but in the path 'export/apps' and if i look into the 'share' folder there's nothing eventhought i cd 'apps', it says "/share/apps: No such file or directory.". So i'm asking you for any advice about this situation that got me confused.
Regards,
Adrian R.
> Date: Wed, 1 Oct 2008 11:41:40 -0500> From: dhosk...@eng.uiowa.edu> To: npaci-rocks...@sdsc.edu> Subject: Re: [Rocks-Discuss] Sharing Apps Directory> > Thanks for the tip.... I hadn't seen that before. I usually make a symlink> to something my users know to keep them from getting confused.> > > On 10/1/08 10:41 AM, "Bart Brashers" <bbra...@Environcorp.com> wrote:> > > If you use the --ghost option, the contents of directories under autofs's> > control will be shown, which is handy for auto-completing and so on. There> > has been some talk of a performance hit in doing this, but I haven't noticed> > any problems on my Rocks 4.1 and Rocks 5.0.3 cluster (same hardware, pre- and> > post-upgrade). Perhaps it's because my cluster is small, only 9 hosts total.> > There's a note about it in the Wiki, but no references or links. I did some> > very quick Googling, and found only a few reference to problems pre-2006, with> > stale NFS handles and user's home directories not being mounted the main> > problems. The lack of post-2006 problems reported to the Rocks list may be> > because they removed the --ghost option starting with Rocks 4.2 (IIRC).> > > > To make the contents visible, make the line in /etc/auto.master look like> > this:> > > > /share /etc/auto.share --ghost --timeout=1200> > > > Bart Brashers> > > >> -----Original Message-----> >> From: npaci-rocks-dis...@sdsc.edu> >> [mailto:npaci-rocks-dis...@sdsc.edu] On> >> Behalf Of David Hoskinson> >> Sent: Wednesday, October 01, 2008 7:53 AM> >> To: Discussion of Rocks Clusters> >> Subject: Re: [Rocks-Discuss] Sharing Apps Directory> >> > >>> From what I am seeing that is the default... Thanks for the path. Stupid> >> hidden folders until you actually navigate to the under nfs got me. I had> >> looked in share but didn't cd to apps. Thanks> >> > >> > >> On 10/1/08 9:03 AM, "Paul Kopec" <pko...@umich.edu> wrote:> >> > >>> The default setup is that /share/apps is on the> >>> frontend and nfs mounted on all the compute nodes under the same name.> >>> > >>> At 09:54 AM 10/1/2008, you wrote:> >>>> On the frontend under the export directory is a folder called apps. In> >>>> this> >>>> folder we have put various apps that we need to do our processing. I don¹t> >>>> see on the compute nodes however a mount for this directory. I do see how> >>>> home is being mounted from the frontend to each compute node. Could> >>>> someone> >>>> let me know how to ³export² the apps directory so its in the same place on> >>>> each compute node. I also see in the exports file under etc that export is> >>>> being nfs shared but when I tried mounting frontend.local:/export/apps it> >>>> didn¹t seem to work.> > > > > > > > This message contains information that may be confidential, privileged or> > otherwise protected by law from disclosure. It is intended for the exclusive> > use of the Addressee(s). Unless you are the addressee or authorized agent of> > the addressee, you may not review, copy, distribute or disclose to anyone the> > message or any information contained within. If you have received this message> > in error, please contact the sender by electronic reply to> > em...@environcorp.com and immediately delete all copies of the message.> >
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Gus Correa
I have Rocks 4.3, so this may not apply to Rocks 5.0, you need to check
it out.
The confusion stems from the fact that /export on the frontend
is just a **soft link** to /state/partition1 (an actual disk partition),
On /state/partition1 there there are several subdirectories, including
home and apps.
The softlink /export is used as a shorthand for /state/partition1,
not surprisingly, to export /state/partition1 to the backend nodes.
By default, only /export (therefore /state/partition1) is exported to
the backend nodes:
myfrontend # cat /etc/exports
/export 10.0.0.0/255.0.0.0(rw,async)
On the backend node side only the "share" and "home" subdirectories
of /state/partition1 (or of /export, if you prefer) are mounted.
They are mounted on /share and /home mountpoints
(not on /export, which doesn't even exist on the backend nodes).
The key files are /etc/auto.master, /etc/auto.share, and /etc/auto.home
compute-0-0 # cat /etc/auto.master
...
/share /etc/auto.share --timeout=1200
/home /etc/auto.home --timeout=1200
compute-0-0 # cat /etc/auto.share
...
apps myfrontend.local:/export/&
install myfrontend.local:/export/home/&
compute-0-0 # cat /etc/auto.home
...
install myfrontend.local:/export/home/&
user1 myfrontend.local:/export/home/user1
user2 myfrontend.local:/export/home/user2
I never use /export to name anything.
This makes my life easier, particularly w.r.t. those things that I want
to use on the backend nodes.
Specifically, when I install applications which use installation scripts
that require a full path name for
the installation directory (typical case: commercial compilers),
I use the /share/apps path, not /export/apps.
Older versions of the Users Guide recommended /export/apps to install
applications.
Fortunately the 5.0 Users Guide now recommends /share/apps:
http://www.rocksclusters.org/roll-documentation/base/5.0/customization-adding-applications.html
Using the path /export/apps instead of /share/apps to install applications
gave me a lot of trouble with shared libraries that would not show up on
the backend nodes,
because their library paths would end up as /export/apps/mysharedlib,
rather than /share/apps/mysharedlib.
To me what is more confusing about /export is that the User's Guide
suggests that /export is an
actual partition, whereas it is in fact a symbolic link to the actual
partition /state/partition1.
http://www.rocksclusters.org/roll-documentation/base/5.0/install-frontend.html
(items 15 and 16)
If you want to create non-default partitions, should you call them
/state/partition1, /state/partition2,
or should you call them /export/partition1, /export/partition2, etc
(as the Users Guide page above seems to suggest)?
I had trouble before when I tried to call them /export/partition2, etc.
I had to reinstall everything.
However, calling them /state/partition1, /state/partition2, etc, worked
fine.
I hope this helps,
Gus Correa
--
---------------------------------------------------------------------
Gustavo J. Ponce Correa, PhD - Email: g...@ldeo.columbia.edu
Lamont-Doherty Earth Observatory - Columbia University
P.O. Box 1000 [61 Route 9W] - Palisades, NY, 10964-8000 - USA
---------------------------------------------------------------------
David Hoskinson
We need to use ghostscript on the compute nodes and I see that it is
installed on frontend but not compute nodes. Using cluster-fork I have
installed ghostscript on all the compute nodes. However I want this to be a
permanent change after reloads. I have put ghostscript and its dependencies
in the extend-compute.xml file which I copied from skeleton.xml.
Notes in the documentation show that I need to run rocks-dist dist from the
home install directory. Is this last step necessary if the packages are
included in the base distro as opposed to rpms that aren't included in
centos or home rolled for example?
Thanks for the bit of help...
Bart Brashers
Yes, it applies the directions you gave in extend-compute.xml. Without
running rocks-dist, you won't change the list of which RPMs should be
installed.
Bart
> -----Original Message-----
> From: npaci-rocks-dis...@sdsc.edu
[mailto:npaci-rocks-dis...@sdsc.edu] On
> Behalf Of David Hoskinson
> Sent: Thursday, October 02, 2008 1:05 PM
> To: Discussion of Rocks Clusters
This message contains information that may be confidential, privileged or otherwise protected by law from disclosure. It is intended for the exclusive use of the Addressee(s). Unless you are the addressee or authorized agent of the addressee, you may not review, copy, distribute or disclose to anyone the message or any information contained within. If you have received this message in error, please contact the sender by electronic reply to em...@environcorp.com and immediately delete all copies of the message.
Mike Hanby
correct terminology?).
Btw, is it required to include all dependency packages in the
<package>somepak</package> section for packages that are part of the
base os roll, or will the kickstart process resolve them automatically
similar to this line in a kickstart file:
%packages --resolvedeps
Thanks, Mike
-----Original Message-----
From: npaci-rocks-dis...@sdsc.edu
[mailto:npaci-rocks-dis...@sdsc.edu] On Behalf Of David
Hoskinson
Sent: Thursday, October 02, 2008 15:05
To: Discussion of Rocks Clusters
dhosk...@eng.uiowa.edu
a new install on a node. It gets all the way through formatting the
partitions, receives setup information and I get a kernel panic. Could
this be my extend-compute.xml? I didn't seem to have any problems with my
dist rebuild.
Bart Brashers
# dbreport kickstart compute-0-0 >! /tmp/ks.cfg
and see if you get any errors. If not, inspect the resulting file for
errors.
Does ghostscript require that X-windows be installed? I don't think so,
but you could/should try this:
# ssh compute-0-1
# cd /home/install/rolls/os/5.0/x86_64/RedHat/RPMS
# rpm -ivh [the list if extra RPMs that you specified in your
extend-compute.xml file]
That will tell you if you have any missing dependencies, and/or other
errors.
Bart
> -----Original Message-----
> From: npaci-rocks-dis...@sdsc.edu
[mailto:npaci-rocks-dis...@sdsc.edu] On
> Behalf Of dhosk...@eng.uiowa.edu
> Sent: Thursday, October 02, 2008 2:29 PM
> To: Discussion of Rocks Clusters
This message contains information that may be confidential, privileged or otherwise protected by law from disclosure. It is intended for the exclusive use of the Addressee(s). Unless you are the addressee or authorized agent of the addressee, you may not review, copy, distribute or disclose to anyone the message or any information contained within. If you have received this message in error, please contact the sender by electronic reply to em...@environcorp.com and immediately delete all copies of the message.
Adrian Robles Ramirez
Thanks for the explanation, it helped me a lot!
Based on your arguments i don't know why i received an error when i run an app distributely:
cp: cannot create regular file `/export/apps/wrf/data/domains/bench_75_75_4/wrf.nl.strc': No such file or directory
if i look into the output file this app generates i see next:
[root@pcwork /]$ tail -f /state/partition1/apps/wrf/runs/bench_75_75_4/rsl.error.0000bash: /export/apps/wrf/bin/wrf_arw_DM.exe: No such file or directoryp0_16936: p4_error: Child process exited while making connection to remote process on compute-0-0.local: 0p0_16936: (6.159948) net_send: could not write to fd=4, errno = 32tail: /state/partition1/apps/wrf/runs/bench_75_75_4/rsl.error.0000: file truncatedbash: /export/apps/wrf/bin/wrf_arw_DM.exe: No such file or directoryp0_17187: p4_error: Child process exited while making connection to remote process on compute-0-0.local: 0p0_17187: (6.165239) net_send: could not write to fd=4, errno = 32
i can ssh the compute node with a password. So what could be wrong, why it says that the path `"/export/apps/wrf/data" does not exist? on the frontend this path does exist!
Regards,
Adrian R.
> Date: Thu, 2 Oct 2008 11:29:36 -0400> From: g...@ldeo.columbia.edu> To: npaci-rocks...@sdsc.edu> Subject: Re: [Rocks-Discuss] Sharing Apps Directory> > Hi Adrian and list> > I have Rocks 4.3, so this may not apply to Rocks 5.0, you need to check > it out.> > The confusion stems from the fact that /export on the frontend> is just a **soft link** to /state/partition1 (an actual disk partition),> On /state/partition1 there there are several subdirectories, including> home and apps. > The softlink /export is used as a shorthand for /state/partition1,> not surprisingly, to export /state/partition1 to the backend nodes.> By default, only /export (therefore /state/partition1) is exported to > the backend nodes:> > myfrontend # cat /etc/exports> /export 10.0.0.0/255.0.0.0(rw,async)> > On the backend node side only the "share" and "home" subdirectories> of /state/partition1 (or of /export, if you prefer) are mounted.> They are mounted on /share and /home mountpoints> (not on /export, which doesn't even exist on the backend nodes).> The key files are /etc/auto.master, /etc/auto.share, and /etc/auto.home> > compute-0-0 # cat /etc/auto.master> ...> /share /etc/auto.share --timeout=1200> /home /etc/auto.home --timeout=1200> > compute-0-0 # cat /etc/auto.share> ...> apps myfrontend.local:/export/&> install myfrontend.local:/export/home/&> > compute-0-0 # cat /etc/auto.home> ...> install myfrontend.local:/export/home/&> user1 myfrontend.local:/export/home/user1> user2 myfrontend.local:/export/home/user2> > I never use /export to name anything.> This makes my life easier, particularly w.r.t. those things that I want > to use on the backend nodes.> Specifically, when I install applications which use installation scripts > that require a full path name for> the installation directory (typical case: commercial compilers),> I use the /share/apps path, not /export/apps.> Older versions of the Users Guide recommended /export/apps to install > applications.> Fortunately the 5.0 Users Guide now recommends /share/apps:> > http://www.rocksclusters.org/roll-documentation/base/5.0/customization-adding-applications.html> > Using the path /export/apps instead of /share/apps to install applications> gave me a lot of trouble with shared libraries that would not show up on > the backend nodes,> because their library paths would end up as /export/apps/mysharedlib,> rather than /share/apps/mysharedlib.> > To me what is more confusing about /export is that the User's Guide > suggests that /export is an> actual partition, whereas it is in fact a symbolic link to the actual > partition /state/partition1.> > http://www.rocksclusters.org/roll-documentation/base/5.0/install-frontend.html > (items 15 and 16)> > If you want to create non-default partitions, should you call them> /state/partition1, /state/partition2,> or should you call them /export/partition1, /export/partition2, etc> (as the Users Guide page above seems to suggest)?> > I had trouble before when I tried to call them /export/partition2, etc.> I had to reinstall everything.> However, calling them /state/partition1, /state/partition2, etc, worked > fine.> > I hope this helps,> Gus Correa> > -- > ---------------------------------------------------------------------> Gustavo J. Ponce Correa, PhD - Email: g...@ldeo.columbia.edu> Lamont-Doherty Earth Observatory - Columbia University> P.O. Box 1000 [61 Route 9W] - Palisades, NY, 10964-8000 - USA> ---------------------------------------------------------------------> > > Adrian Robles Ramirez wrote:> > >Hi everybody,> > > >i didn't see the complete answer so i still having a doubt. In my case in the frontend i can see that 'export' is a autofs directory and i also see the 'share' folder. On the node side i just see the the 'share' folder and i can access it and see that exists the 'apps' folder. Into that folder there are all the apps i have installed. However on the frontend side i see the same folder structure but in the path 'export/apps' and if i look into the 'share' folder there's nothing eventhought i cd 'apps', it says "/share/apps: No such file or directory.". So i'm asking you for any advice about this situation that got me confused.> > > >Regards,> > > >Adrian R.> > > > > >> >>Date: Wed, 1 Oct 2008 11:41:40 -0500> From: dhosk...@eng.uiowa.edu> To: npaci-rocks...@sdsc.edu> Subject: Re: [Rocks-Discuss] Sharing Apps Directory> > Thanks for the tip.... I hadn't seen that before. I usually make a symlink> to something my users know to keep them from getting confused.> > > On 10/1/08 10:41 AM, "Bart Brashers" <bbra...@Environcorp.com> wrote:> > > If you use the --ghost option, the contents of directories under autofs's> > control will be shown, which is handy for auto-completing and so on. There> > has been some talk of a performance hit in doing this, but I haven't noticed> > any problems on my Rocks 4.1 and Rocks 5.0.3 cluster (same hardware, pre- and> > post-upgrade). Perhaps it's because my cluster is small, only 9 hosts total.> > There's a note about it in the Wiki, but no references or links. I did some> > very quick Googling, and found only a few reference to problems pre-2006, with> > stale NFS handles and user's home directories not being mounted the main> > problems. The lack of post-2006 problems reported to the Rocks list may be> > because they removed the --ghost option starting with Rocks 4.2 (IIRC).> > > > To make the contents visible, make the line in /etc/auto.master look like> > this:> > > > /share /etc/auto.share --ghost --timeout=1200> > > > Bart Brashers> > > >> -----Original Message-----> >> From: npaci-rocks-dis...@sdsc.edu> >> [mailto:npaci-rocks-dis...@sdsc.edu] On> >> Behalf Of David Hoskinson> >> Sent: Wednesday, October 01, 2008 7:53 AM> >> To: Discussion of Rocks Clusters> >> Subject: Re: [Rocks-Discuss] Sharing Apps Directory> >> > >>> From what I am seeing that is the default... Thanks for the path. Stupid> >> hidden folders until you actually navigate to the under nfs got me. I had> >> looked in share but didn't cd to apps. Thanks> >> > >> > >> On 10/1/08 9:03 AM, "Paul Kopec" <pko...@umich.edu> wrote:> >> > >>> The default setup is that /share/apps is on the> >>> frontend and nfs mounted on all the compute nodes under the same name.> >>> > >>> At 09:54 AM 10/1/2008, you wrote:> >>>> On the frontend under the export directory is a folder called apps. In> >>>> this> >>>> folder we have put various apps that we need to do our processing. I don¹t> >>>> see on the compute nodes however a mount for this directory. I do see how> >>>> home is being mounted from the frontend to each compute node. Could> >>>> someone> >>>> let me know how to ³export² the apps directory so its in the same place on> >>>> each compute node. I also see in the exports file under etc that export is> >>>> being nfs shared but when I tried mounting frontend.local:/export/apps it> >>>> didn¹t seem to work.> > > > > > > > This message contains information that may be confidential, privileged or> > otherwise protected by law from disclosure. It is intended for the exclusive> > use of the Addressee(s). Unless you are the addressee or authorized agent of> > the addressee, you may not review, copy, distribute or disclose to anyone the> > message or any information contained within. If you have received this message> > in error, please contact the sender by electronic reply to> > em...@environcorp.com and immediately delete all copies of the message.> > > >> > >>> >_________________________________________________________________> >Appelez vos amis de PC à PC -- C'EST GRATUIT> >http://get.live.com/messenger/overview> >-------------- next part --------------> >An HTML attachment was scrubbed...> >URL: https://lists.sdsc.edu/pipermail/npaci-rocks-discussion/attachments/20081001/9550ef19/attachment.html > > > >> >
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David Hoskinson
and rebuilt rocks-dist and the install worked fine so there may be a syntax
error in my file. It does not require xwindows as I installed manually on
one machine and copied the list of dependencies from there.
Bart Brashers
Bart
> -----Original Message-----
> From: npaci-rocks-dis...@sdsc.edu [mailto:npaci-rocks-dis...@sdsc.edu] On
> Behalf Of Adrian Robles Ramirez
> Sent: Friday, October 03, 2008 1:20 PM
> To: Discussion of Rocks Clusters
> Subject: Re: [Rocks-Discuss] Sharing Apps Directory
>
>
> Thanks for the explanation, it helped me a lot!
>
> Based on your arguments i don't know why i received an error when i run an app distributely:
>
> cp: cannot create regular file `/export/apps/wrf/data/domains/bench_75_75_4/wrf.nl.strc': No such
> file or directory
>
> if i look into the output file this app generates i see next:
>
> [root@pcwork /]$ tail -f /state/partition1/apps/wrf/runs/bench_75_75_4/rsl.error.0000bash:
> /export/apps/wrf/bin/wrf_arw_DM.exe: No such file or directoryp0_16936: p4_error: Child process
> exited while making connection to remote process on compute-0-0.local: 0p0_16936: (6.159948)
> net_send: could not write to fd=4, errno = 32tail:
> /state/partition1/apps/wrf/runs/bench_75_75_4/rsl.error.0000: file truncatedbash:
> /export/apps/wrf/bin/wrf_arw_DM.exe: No such file or directoryp0_17187: p4_error: Child process
> exited while making connection to remote process on compute-0-0.local: 0p0_17187: (6.165239)
> net_send: could not write to fd=4, errno = 32
> i can ssh the compute node with a password. So what could be wrong, why it says that the path
> `"/export/apps/wrf/data" does not exist? on the frontend this path does exist!
>
> Regards,
>
> Adrian R.
>
>
> > Date: Thu, 2 Oct 2008 11:29:36 -0400> From: g...@ldeo.columbia.edu> To: npaci-rocks-
> discu...@sdsc.edu> Subject: Re: [Rocks-Discuss] Sharing Apps Directory> > Hi Adrian and list> > I
Gus Correa
Your application should refer to /share/apps, instead of /export/apps.
It is just as I and others said to you:
/export/apps only exists on the frontend, not on the compute nodes.
Better never use /export/home/username or /export/apps
in full path names on programs that run in the compute nodes.
Use /home/username and /share/apps instead.
I hope this helps,
Gus Correa
Adrian Robles Ramirez
Thanks again.
Adrian R.
> Date: Fri, 3 Oct 2008 18:20:27 -0400> From: g...@ldeo.columbia.edu> To: npaci-rocks...@sdsc.edu> Subject: Re: [Rocks-Discuss] Sharing Apps Directory> > Hi Adrian and list> > Your application should refer to /share/apps, instead of /export/apps.> It is just as I and others said to you:> /export/apps only exists on the frontend, not on the compute nodes.> > Better never use /export/home/username or /export/apps> in full path names on programs that run in the compute nodes.> Use /home/username and /share/apps instead.> > I hope this helps,> Gus Correa> > Adrian Robles Ramirez wrote:> > >Thanks for the explanation, it helped me a lot!> > > >Based on your arguments i don't know why i received an error when i run an app distributely:> > > >cp: cannot create regular file `/export/apps/wrf/data/domains/bench_75_75_4/wrf.nl.strc': No such file or directory> > > >if i look into the output file this app generates i see next:> > > >[root@pcwork /]$ tail -f /state/partition1/apps/wrf/runs/bench_75_75_4/rsl.error.0000bash: /export/apps/wrf/bin/wrf_arw_DM.exe: No such file or directoryp0_16936: p4_error: Child process exited while making connection to remote process on compute-0-0.local: 0p0_16936: (6.159948) net_send: could not write to fd=4, errno = 32tail: /state/partition1/apps/wrf/runs/bench_75_75_4/rsl.error.0000: file truncatedbash: /export/apps/wrf/bin/wrf_arw_DM.exe: No such file or directoryp0_17187: p4_error: Child process exited while making connection to remote process on compute-0-0.local: 0p0_17187: (6.165239) net_send: could not write to fd=4, errno = 32 > >i can ssh the compute node with a password. So what could be wrong, why it says that the path `"/export/apps/wrf/data" does not exist? on the frontend this path does exist!> > > >Regards,> > > >Adrian R.> > > > > > > >> >>Date: Thu, 2 Oct 2008 11:29:36 -0400> From: g...@ldeo.columbia.edu> To: npaci-rocks...@sdsc.edu> Subject: Re: [Rocks-Discuss] Sharing Apps Directory> > Hi Adrian and list> > I have Rocks 4.3, so this may not apply to Rocks 5.0, you need to check > it out.> > The confusion stems from the fact that /export on the frontend> is just a **soft link** to /state/partition1 (an actual disk partition),> On /state/partition1 there there are several subdirectories, including> home and apps. > The softlink /export is used as a shorthand for /state/partition1,> not surprisingly, to export /state/partition1 to the backend nodes.> By default, only /export (therefore /state/partition1) is exported to > the backend nodes:> > myfrontend # cat /etc/exports> /export 10.0.0.0/255.0.0.0(rw,async)> > On the backend node side only the "share" and "home" subdirectories> of /state/partition1 (or of /export, if you prefer) are mounted.> They are mounted on /share and /home mountpoints> (not on /export, which doesn't even exist on the backend nodes).> The key files are /etc/auto.master, /etc/auto.share, and /etc/auto.home> > compute-0-0 # cat /etc/auto.master> ...> /share /etc/auto.share --timeout=1200> /home /etc/auto.home --timeout=1200> > compute-0-0 # cat /etc/auto.share> ...> apps myfrontend.local:/export/&> install myfrontend.local:/export/home/&> > compute-0-0 # cat /etc/auto.home> ...> install myfrontend.local:/export/home/&> user1 myfrontend.local:/export/home/user1> user2 myfrontend.local:/export/home/user2> > I never use /export to name anything.> This makes my life easier, particularly w.r.t. those things that I want > to use on the backend nodes.> Specifically, when I install applications which use installation scripts > that require a full path name for> the installation directory (typical case: commercial compilers),> I use the /share/apps path, not /export/apps.> Older versions of the Users Guide recommended /export/apps to install > applications.> Fortunately the 5.0 Users Guide now recommends /share/apps:> > http://www.rocksclusters.org/roll-documentation/base/5.0/customization-adding-applications.html> > Using the path /export/apps instead of /share/apps to install applications> gave me a lot of trouble with shared libraries that would not show up on > the backend nodes,> because their library paths would end up as /export/apps/mysharedlib,> rather than /share/apps/mysharedlib.> > To me what is more confusing about /export is that the User's Guide > suggests that /export is an> actual partition, whereas it is in fact a symbolic link to the actual > partition /state/partition1.> > http://www.rocksclusters.org/roll-documentation/base/5.0/install-frontend.html > (items 15 and 16)> > If you want to create non-default partitions, should you call them> /state/partition1, /state/partition2,> or should you call them /export/partition1, /export/partition2, etc> (as the Users Guide page above seems to suggest)?> > I had trouble before when I tried to call them /export/partition2, etc.> I had to reinstall everything.> However, calling them /state/partition1, /state/partition2, etc, worked > fine.> > I hope this helps,> Gus Correa> > -- > ---------------------------------------------------------------------> Gustavo J. Ponce Correa, PhD - Email: g...@ldeo.columbia.edu> Lamont-Doherty Earth Observatory - Columbia University> P.O. Box 1000 [61 Route 9W] - Palisades, NY, 10964-8000 - USA> ---------------------------------------------------------------------> > > Adrian Robles Ramirez wrote:> > >Hi everybody,> > > >i didn't see the complete answer so i still having a doubt. In my case in the frontend i can see that 'export' is a autofs directory and i also see the 'share' folder. On the node side i just see the the 'share' folder and i can access it and see that exists the 'apps' folder. Into that folder there are all the apps i have installed. However on the frontend side i see the same folder structure but in the path 'export/apps' and if i look into the 'share' folder there's nothing eventhought i cd 'apps', it says "/share/apps: No such file or directory.". So i'm asking you for any advice about this situation that got me confused.> > > >Regards,> > > >Adrian R.> > > > > >> >>Date: Wed, 1 Oct 2008 11:41:40 -0500> From: dhosk...@eng.uiowa.edu> To: npaci-rocks...@sdsc.edu> Subject: Re: [Rocks-Discuss] Sharing Apps Directory> > Thanks for the tip.... I hadn't seen that before. I usually make a symlink> to something my users know to keep them from getting confused.> > > On 10/1/08 10:41 AM, "Bart Brashers" <bbra...@Environcorp.com> wrote:> > > If you use the --ghost option, the contents of directories under autofs's> > control will be shown, which is handy for auto-completing and so on. There> > has been some talk of a performance hit in doing this, but I haven't noticed> > any problems on my Rocks 4.1 and Rocks 5.0.3 cluster (same hardware, pre- and> > post-upgrade). Perhaps it's because my cluster is small, only 9 hosts total.> > There's a note about it in the Wiki, but no references or links. I did some> > very quick Googling, and found only a few reference to problems pre-2006, with> > stale NFS handles and user's home directories not being mounted the main> > problems. The lack of post-2006 problems reported to the Rocks list may be> > because they removed the --ghost option starting with Rocks 4.2 (IIRC).> > > > To make the contents visible, make the line in /etc/auto.master look like> > this:> > > > /share /etc/auto.share --ghost --timeout=1200> > > > Bart Brashers> > > >> -----Original Message-----> >> From: npaci-rocks-dis...@sdsc.edu> >> [mailto:npaci-rocks-dis...@sdsc.edu] On> >> Behalf Of David Hoskinson> >> Sent: Wednesday, October 01, 2008 7:53 AM> >> To: Discussion of Rocks Clusters> >> Subject: Re: [Rocks-Discuss] Sharing Apps Directory> >> > >>> From what I am seeing that is the default... Thanks for the path. Stupid> >> hidden folders until you actually navigate to the under nfs got me. I had> >> looked in share but didn't cd to apps. Thanks> >> > >> > >> On 10/1/08 9:03 AM, "Paul Kopec" <pko...@umich.edu> wrote:> >> > >>> The default setup is that /share/apps is on the> >>> frontend and nfs mounted on all the compute nodes under the same name.> >>> > >>> At 09:54 AM 10/1/2008, you wrote:> >>>> On the frontend under the export directory is a folder called apps. In> >>>> this> >>>> folder we have put various apps that we need to do our processing. I don¹t> >>>> see on the compute nodes however a mount for this directory. I do see how> >>>> home is being mounted from the frontend to each compute node. Could> >>>> someone> >>>> let me know how to ³export² the apps directory so its in the same place on> >>>> each compute node. I also see in the exports file under etc that export is> >>>> being nfs shared but when I tried mounting frontend.local:/export/apps it> >>>> didn¹t seem to work.> > > > > > > > This message contains information that may be confidential, privileged or> > otherwise protected by law from disclosure. It is intended for the exclusive> > use of the Addressee(s). Unless you are the addressee or authorized agent of> > the addressee, you may not review, copy, distribute or disclose to anyone the> > message or any information contained within. If you have received this message> > in error, please contact the sender by electronic reply to> > em...@environcorp.com and immediately delete all copies of the message.> > > >> > >>> >_________________________________________________________________> >Appelez vos amis de PC à PC -- C'EST GRATUIT> >http://get.live.com/messenger/overview> >-------------- next part --------------> >An HTML attachment was scrubbed...> >URL: https://lists.sdsc.edu/pipermail/npaci-rocks-discussion/attachments/20081001/9550ef19/attachment.html > > > >> > > >> > >>> >_________________________________________________________________> >Téléchargez le nouveau Windows Live Messenger !> >http://get.live.com/messenger/overview> >-------------- next part --------------> >An HTML attachment was scrubbed...> >URL: https://lists.sdsc.edu/pipermail/npaci-rocks-discussion/attachments/20081003/efcda106/attachment.html > > > >> >
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