Cluster Install - Trouble finding drmaa egg
I'm trying to install Galaxy on our SGE cluster (using the Unified method). I installed galaxy-dist, and now I'm on this section: drmaa egg The drmaa egg is provided by Galaxy, but you must tell it where your resource manager's DRMAA library is located, and this is done with the $DRMAA_LIBRARY_PATH environment variable: % export DRMAA_LIBRARY_PATH=/galaxy/lsf/7.0/linux2.6-glibc2.3-x86_64/lib/libdrmaa.so.1.0.3 % export DRMAA_LIBRARY_PATH=/galaxy/sge/lib/lx24-amd64/libdrmaa.so.1.0 However I can't locate the the file libdrmaa.so.1.0.3 anywhere. In fact I don't have have an lsf nor sge directory within galaxy-dist. Thanks, Greg
Have you installed SGE on the same machine? If so, then you should be able to do a "locate libdrmaa.so", which should point to SGE's DRMAA library. For example, on a machine that I use, I see this: $ locate libdrmaa.so /usr/lib/libdrmaa.so /usr/lib/libdrmaa.so.1.0 $ ls /usr/lib/libdrmaa* /usr/lib/libdrmaa.so /usr/lib/libdrmaa.so.1.0 $ ls -la /usr/lib/libdrmaa.so lrwxrwxrwx 1 root root 15 Apr 18 2012 /usr/lib/libdrmaa.so -> libdrmaa.so.1.0 You may also want to try "updatedb" (again, assuming you're using Linux) to index the files on your machine. Finally, if you can't find it, then you should check if you actually have SGE installed on that machine. I like to use "dpkg" on Ubuntu/Debian and "yum" on Centos to manipulate packages. -Scott ----- Original Message -----
I'm trying to install Galaxy on our SGE cluster (using the Unified method).
I installed galaxy-dist, and now I'm on this section:
drmaa egg
The drmaa egg is provided by Galaxy, but you must tell it where your resource manager's DRMAA library is located, and this is done with the $DRMAA_LIBRARY_PATH environment variable: % export DRMAA_LIBRARY_PATH=/galaxy/lsf/7.0/linux2.6-glibc2.3-x86_64/lib/libdrmaa.so.1.0.3 % export DRMAA_LIBRARY_PATH=/galaxy/sge/lib/lx24-amd64/libdrmaa.so.1.0
However I can't locate the the file libdrmaa.so.1.0.3 anywhere. In fact I don't have have an lsf nor sge directory within galaxy-dist.
Thanks,
Greg ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
I forgot to add my value of DRMAA_LIBRARY_PATH. Note that I just need DRMAA_LIBRARY_PATH to point to the library being used. So in the example below, I had this:
echo $DRMAA_LIBRARY_PATH /usr/lib/libdrmaa.so
-Scott ----- Original Message -----
Have you installed SGE on the same machine? If so, then you should be able to do a "locate libdrmaa.so", which should point to SGE's DRMAA library. For example, on a machine that I use, I see this:
$ locate libdrmaa.so /usr/lib/libdrmaa.so /usr/lib/libdrmaa.so.1.0 $ ls /usr/lib/libdrmaa* /usr/lib/libdrmaa.so /usr/lib/libdrmaa.so.1.0 $ ls -la /usr/lib/libdrmaa.so lrwxrwxrwx 1 root root 15 Apr 18 2012 /usr/lib/libdrmaa.so -> libdrmaa.so.1.0
You may also want to try "updatedb" (again, assuming you're using Linux) to index the files on your machine. Finally, if you can't find it, then you should check if you actually have SGE installed on that machine. I like to use "dpkg" on Ubuntu/Debian and "yum" on Centos to manipulate packages.
-Scott
----- Original Message -----
I'm trying to install Galaxy on our SGE cluster (using the Unified method).
I installed galaxy-dist, and now I'm on this section:
drmaa egg
The drmaa egg is provided by Galaxy, but you must tell it where your resource manager's DRMAA library is located, and this is done with the $DRMAA_LIBRARY_PATH environment variable: % export DRMAA_LIBRARY_PATH=/galaxy/lsf/7.0/linux2.6-glibc2.3-x86_64/lib/libdrmaa.so.1.0.3
% export DRMAA_LIBRARY_PATH=/galaxy/sge/lib/lx24-amd64/libdrmaa.so.1.0
However I can't locate the the file libdrmaa.so.1.0.3 anywhere. In fact I don't have have an lsf nor sge directory within galaxy-dist.
Thanks,
Greg
___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org. Please keep all replies on the list by
using "reply all" in your mail client. For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:
To manage your subscriptions to this and other Galaxy lists,
please use the interface at:
___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
Thanks Scott. I did turn up: /sge/8.0.1p4/lib/lx-amd64/libdrmaa.so.1.0 I guess that would be it. For a followup question ,how do I make the DRMAA_LIBRARY_PATH variable permanent on the machine? -Greg On Mon, Nov 5, 2012 at 3:03 PM, Scott McManus <scottmcmanus@gatech.edu>wrote:
I forgot to add my value of DRMAA_LIBRARY_PATH. Note that I just need DRMAA_LIBRARY_PATH to point to the library being used. So in the example below, I had this:
*echo $DRMAA_LIBRARY_PATH* /usr/lib/libdrmaa.so
-Scott
------------------------------
Have you installed SGE on the same machine? If so, then you should be able to do a "locate libdrmaa.so", which should point to SGE's DRMAA library. For example, on a machine that I use, I see this:
$ locate libdrmaa.so /usr/lib/libdrmaa.so /usr/lib/libdrmaa.so.1.0 $ ls /usr/lib/libdrmaa* /usr/lib/libdrmaa.so /usr/lib/libdrmaa.so.1.0 $ ls -la /usr/lib/libdrmaa.so lrwxrwxrwx 1 root root 15 Apr 18 2012 /usr/lib/libdrmaa.so -> libdrmaa.so.1.0
You may also want to try "updatedb" (again, assuming you're using Linux) to index the files on your machine. Finally, if you can't find it, then you should check if you actually have SGE installed on that machine. I like to use "dpkg" on Ubuntu/Debian and "yum" on Centos to manipulate packages.
-Scott
------------------------------
I'm trying to install Galaxy on our SGE cluster (using the Unified method).
I installed galaxy-dist, and now I'm on this section:
drmaa egg
The drmaa egg is provided by Galaxy, but you must tell it where your resource manager's DRMAA library is located, and this is done with the $DRMAA_LIBRARY_PATH environment variable:
% export DRMAA_LIBRARY_PATH=/galaxy/lsf/7.0/linux2.6-glibc2.3-x86_64/lib/libdrmaa.so.1.0.3 % export DRMAA_LIBRARY_PATH=/galaxy/sge/lib/lx24-amd64/libdrmaa.so.1.0
However I can't locate the the file libdrmaa.so.1.0.3 anywhere. In fact I don't have have an lsf nor sge directory within galaxy-dist.
Thanks,
Greg
___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
And am I correct in the thinking that only the machine hosting the galaxy web interface and submitting jobs needs the export DRMAA_LIBRARY_PATH= variable? The normal nodes running jobs don't need this, right? Thanks, -Greg On Mon, Nov 5, 2012 at 3:12 PM, greg <margeemail@gmail.com> wrote:
Thanks Scott. I did turn up: /sge/8.0.1p4/lib/lx-amd64/libdrmaa.so.1.0
I guess that would be it.
For a followup question ,how do I make the DRMAA_LIBRARY_PATH variable permanent on the machine?
-Greg
On Mon, Nov 5, 2012 at 3:03 PM, Scott McManus <scottmcmanus@gatech.edu> wrote:
I forgot to add my value of DRMAA_LIBRARY_PATH. Note that I just need DRMAA_LIBRARY_PATH to point to the library being used. So in the example below, I had this:
echo $DRMAA_LIBRARY_PATH /usr/lib/libdrmaa.so
-Scott
________________________________
Have you installed SGE on the same machine? If so, then you should be able to do a "locate libdrmaa.so", which should point to SGE's DRMAA library. For example, on a machine that I use, I see this:
$ locate libdrmaa.so /usr/lib/libdrmaa.so /usr/lib/libdrmaa.so.1.0 $ ls /usr/lib/libdrmaa* /usr/lib/libdrmaa.so /usr/lib/libdrmaa.so.1.0 $ ls -la /usr/lib/libdrmaa.so lrwxrwxrwx 1 root root 15 Apr 18 2012 /usr/lib/libdrmaa.so -> libdrmaa.so.1.0
You may also want to try "updatedb" (again, assuming you're using Linux) to index the files on your machine. Finally, if you can't find it, then you should check if you actually have SGE installed on that machine. I like to use "dpkg" on Ubuntu/Debian and "yum" on Centos to manipulate packages.
-Scott
________________________________
I'm trying to install Galaxy on our SGE cluster (using the Unified method).
I installed galaxy-dist, and now I'm on this section:
drmaa egg
The drmaa egg is provided by Galaxy, but you must tell it where your resource manager's DRMAA library is located, and this is done with the$DRMAA_LIBRARY_PATH environment variable:
% export DRMAA_LIBRARY_PATH=/galaxy/lsf/7.0/linux2.6-glibc2.3-x86_64/lib/libdrmaa.so.1.0.3 % export DRMAA_LIBRARY_PATH=/galaxy/sge/lib/lx24-amd64/libdrmaa.so.1.0
However I can't locate the the file libdrmaa.so.1.0.3 anywhere. In fact I don't have have an lsf nor sge directory within galaxy-dist.
Thanks,
Greg
___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
On Nov 5, 2012, at 3:15 PM, greg wrote:
And am I correct in the thinking that only the machine hosting the galaxy web interface and submitting jobs needs the export DRMAA_LIBRARY_PATH= variable?
The normal nodes running jobs don't need this, right?
Hi Greg, That's correct. If you're starting Galaxy with an init script, I'd put the export there. --nate
Thanks,
-Greg
On Mon, Nov 5, 2012 at 3:12 PM, greg <margeemail@gmail.com> wrote:
Thanks Scott. I did turn up: /sge/8.0.1p4/lib/lx-amd64/libdrmaa.so.1.0
I guess that would be it.
For a followup question ,how do I make the DRMAA_LIBRARY_PATH variable permanent on the machine?
-Greg
On Mon, Nov 5, 2012 at 3:03 PM, Scott McManus <scottmcmanus@gatech.edu> wrote:
I forgot to add my value of DRMAA_LIBRARY_PATH. Note that I just need DRMAA_LIBRARY_PATH to point to the library being used. So in the example below, I had this:
echo $DRMAA_LIBRARY_PATH /usr/lib/libdrmaa.so
-Scott
________________________________
Have you installed SGE on the same machine? If so, then you should be able to do a "locate libdrmaa.so", which should point to SGE's DRMAA library. For example, on a machine that I use, I see this:
$ locate libdrmaa.so /usr/lib/libdrmaa.so /usr/lib/libdrmaa.so.1.0 $ ls /usr/lib/libdrmaa* /usr/lib/libdrmaa.so /usr/lib/libdrmaa.so.1.0 $ ls -la /usr/lib/libdrmaa.so lrwxrwxrwx 1 root root 15 Apr 18 2012 /usr/lib/libdrmaa.so -> libdrmaa.so.1.0
You may also want to try "updatedb" (again, assuming you're using Linux) to index the files on your machine. Finally, if you can't find it, then you should check if you actually have SGE installed on that machine. I like to use "dpkg" on Ubuntu/Debian and "yum" on Centos to manipulate packages.
-Scott
________________________________
I'm trying to install Galaxy on our SGE cluster (using the Unified method).
I installed galaxy-dist, and now I'm on this section:
drmaa egg
The drmaa egg is provided by Galaxy, but you must tell it where your resource manager's DRMAA library is located, and this is done with the$DRMAA_LIBRARY_PATH environment variable:
% export DRMAA_LIBRARY_PATH=/galaxy/lsf/7.0/linux2.6-glibc2.3-x86_64/lib/libdrmaa.so.1.0.3 % export DRMAA_LIBRARY_PATH=/galaxy/sge/lib/lx24-amd64/libdrmaa.so.1.0
However I can't locate the the file libdrmaa.so.1.0.3 anywhere. In fact I don't have have an lsf nor sge directory within galaxy-dist.
Thanks,
Greg
___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
Well, I want it to ultimately run under Apache. Does it still make sense to go in an init script? thanks again, Greg On Mon, Nov 5, 2012 at 3:23 PM, Nate Coraor <nate@bx.psu.edu> wrote:
On Nov 5, 2012, at 3:15 PM, greg wrote:
And am I correct in the thinking that only the machine hosting the galaxy web interface and submitting jobs needs the export DRMAA_LIBRARY_PATH= variable?
The normal nodes running jobs don't need this, right?
Hi Greg,
That's correct. If you're starting Galaxy with an init script, I'd put the export there.
--nate
Thanks,
-Greg
On Mon, Nov 5, 2012 at 3:12 PM, greg <margeemail@gmail.com> wrote:
Thanks Scott. I did turn up: /sge/8.0.1p4/lib/lx-amd64/libdrmaa.so.1.0
I guess that would be it.
For a followup question ,how do I make the DRMAA_LIBRARY_PATH variable permanent on the machine?
-Greg
On Mon, Nov 5, 2012 at 3:03 PM, Scott McManus <scottmcmanus@gatech.edu> wrote:
I forgot to add my value of DRMAA_LIBRARY_PATH. Note that I just need DRMAA_LIBRARY_PATH to point to the library being used. So in the example below, I had this:
echo $DRMAA_LIBRARY_PATH /usr/lib/libdrmaa.so
-Scott
________________________________
Have you installed SGE on the same machine? If so, then you should be able to do a "locate libdrmaa.so", which should point to SGE's DRMAA library. For example, on a machine that I use, I see this:
$ locate libdrmaa.so /usr/lib/libdrmaa.so /usr/lib/libdrmaa.so.1.0 $ ls /usr/lib/libdrmaa* /usr/lib/libdrmaa.so /usr/lib/libdrmaa.so.1.0 $ ls -la /usr/lib/libdrmaa.so lrwxrwxrwx 1 root root 15 Apr 18 2012 /usr/lib/libdrmaa.so -> libdrmaa.so.1.0
You may also want to try "updatedb" (again, assuming you're using Linux) to index the files on your machine. Finally, if you can't find it, then you should check if you actually have SGE installed on that machine. I like to use "dpkg" on Ubuntu/Debian and "yum" on Centos to manipulate packages.
-Scott
________________________________
I'm trying to install Galaxy on our SGE cluster (using the Unified method).
I installed galaxy-dist, and now I'm on this section:
drmaa egg
The drmaa egg is provided by Galaxy, but you must tell it where your resource manager's DRMAA library is located, and this is done with the$DRMAA_LIBRARY_PATH environment variable:
% export DRMAA_LIBRARY_PATH=/galaxy/lsf/7.0/linux2.6-glibc2.3-x86_64/lib/libdrmaa.so.1.0.3 % export DRMAA_LIBRARY_PATH=/galaxy/sge/lib/lx24-amd64/libdrmaa.so.1.0
However I can't locate the the file libdrmaa.so.1.0.3 anywhere. In fact I don't have have an lsf nor sge directory within galaxy-dist.
Thanks,
Greg
___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
On Nov 5, 2012, at 3:26 PM, greg wrote:
Well, I want it to ultimately run under Apache. Does it still make sense to go in an init script?
thanks again,
Yes, even when running behind Apache, you'll need an init script (or similar method) to start the Galaxy server. --nate
Greg
On Mon, Nov 5, 2012 at 3:23 PM, Nate Coraor <nate@bx.psu.edu> wrote:
On Nov 5, 2012, at 3:15 PM, greg wrote:
And am I correct in the thinking that only the machine hosting the galaxy web interface and submitting jobs needs the export DRMAA_LIBRARY_PATH= variable?
The normal nodes running jobs don't need this, right?
Hi Greg,
That's correct. If you're starting Galaxy with an init script, I'd put the export there.
--nate
Thanks,
-Greg
On Mon, Nov 5, 2012 at 3:12 PM, greg <margeemail@gmail.com> wrote:
Thanks Scott. I did turn up: /sge/8.0.1p4/lib/lx-amd64/libdrmaa.so.1.0
I guess that would be it.
For a followup question ,how do I make the DRMAA_LIBRARY_PATH variable permanent on the machine?
-Greg
On Mon, Nov 5, 2012 at 3:03 PM, Scott McManus <scottmcmanus@gatech.edu> wrote:
I forgot to add my value of DRMAA_LIBRARY_PATH. Note that I just need DRMAA_LIBRARY_PATH to point to the library being used. So in the example below, I had this:
echo $DRMAA_LIBRARY_PATH /usr/lib/libdrmaa.so
-Scott
________________________________
Have you installed SGE on the same machine? If so, then you should be able to do a "locate libdrmaa.so", which should point to SGE's DRMAA library. For example, on a machine that I use, I see this:
$ locate libdrmaa.so /usr/lib/libdrmaa.so /usr/lib/libdrmaa.so.1.0 $ ls /usr/lib/libdrmaa* /usr/lib/libdrmaa.so /usr/lib/libdrmaa.so.1.0 $ ls -la /usr/lib/libdrmaa.so lrwxrwxrwx 1 root root 15 Apr 18 2012 /usr/lib/libdrmaa.so -> libdrmaa.so.1.0
You may also want to try "updatedb" (again, assuming you're using Linux) to index the files on your machine. Finally, if you can't find it, then you should check if you actually have SGE installed on that machine. I like to use "dpkg" on Ubuntu/Debian and "yum" on Centos to manipulate packages.
-Scott
________________________________
I'm trying to install Galaxy on our SGE cluster (using the Unified method).
I installed galaxy-dist, and now I'm on this section:
drmaa egg
The drmaa egg is provided by Galaxy, but you must tell it where your resource manager's DRMAA library is located, and this is done with the$DRMAA_LIBRARY_PATH environment variable:
% export DRMAA_LIBRARY_PATH=/galaxy/lsf/7.0/linux2.6-glibc2.3-x86_64/lib/libdrmaa.so.1.0.3 % export DRMAA_LIBRARY_PATH=/galaxy/sge/lib/lx24-amd64/libdrmaa.so.1.0
However I can't locate the the file libdrmaa.so.1.0.3 anywhere. In fact I don't have have an lsf nor sge directory within galaxy-dist.
Thanks,
Greg
___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
Ok, that makes sense. Would you mind sharing how you set up your init script? What goes in it, where you place it? Thanks again, Greg On Mon, Nov 5, 2012 at 3:33 PM, Nate Coraor <nate@bx.psu.edu> wrote:
On Nov 5, 2012, at 3:26 PM, greg wrote:
Well, I want it to ultimately run under Apache. Does it still make sense to go in an init script?
thanks again,
Yes, even when running behind Apache, you'll need an init script (or similar method) to start the Galaxy server.
--nate
Greg
On Mon, Nov 5, 2012 at 3:23 PM, Nate Coraor <nate@bx.psu.edu> wrote:
On Nov 5, 2012, at 3:15 PM, greg wrote:
And am I correct in the thinking that only the machine hosting the galaxy web interface and submitting jobs needs the export DRMAA_LIBRARY_PATH= variable?
The normal nodes running jobs don't need this, right?
Hi Greg,
That's correct. If you're starting Galaxy with an init script, I'd put the export there.
--nate
Thanks,
-Greg
On Mon, Nov 5, 2012 at 3:12 PM, greg <margeemail@gmail.com> wrote:
Thanks Scott. I did turn up: /sge/8.0.1p4/lib/lx-amd64/libdrmaa.so.1.0
I guess that would be it.
For a followup question ,how do I make the DRMAA_LIBRARY_PATH variable permanent on the machine?
-Greg
On Mon, Nov 5, 2012 at 3:03 PM, Scott McManus <scottmcmanus@gatech.edu> wrote:
I forgot to add my value of DRMAA_LIBRARY_PATH. Note that I just need DRMAA_LIBRARY_PATH to point to the library being used. So in the example below, I had this:
> echo $DRMAA_LIBRARY_PATH /usr/lib/libdrmaa.so
-Scott
________________________________
Have you installed SGE on the same machine? If so, then you should be able to do a "locate libdrmaa.so", which should point to SGE's DRMAA library. For example, on a machine that I use, I see this:
$ locate libdrmaa.so /usr/lib/libdrmaa.so /usr/lib/libdrmaa.so.1.0 $ ls /usr/lib/libdrmaa* /usr/lib/libdrmaa.so /usr/lib/libdrmaa.so.1.0 $ ls -la /usr/lib/libdrmaa.so lrwxrwxrwx 1 root root 15 Apr 18 2012 /usr/lib/libdrmaa.so -> libdrmaa.so.1.0
You may also want to try "updatedb" (again, assuming you're using Linux) to index the files on your machine. Finally, if you can't find it, then you should check if you actually have SGE installed on that machine. I like to use "dpkg" on Ubuntu/Debian and "yum" on Centos to manipulate packages.
-Scott
________________________________
I'm trying to install Galaxy on our SGE cluster (using the Unified method).
I installed galaxy-dist, and now I'm on this section:
drmaa egg
The drmaa egg is provided by Galaxy, but you must tell it where your resource manager's DRMAA library is located, and this is done with the$DRMAA_LIBRARY_PATH environment variable:
% export DRMAA_LIBRARY_PATH=/galaxy/lsf/7.0/linux2.6-glibc2.3-x86_64/lib/libdrmaa.so.1.0.3 % export DRMAA_LIBRARY_PATH=/galaxy/sge/lib/lx24-amd64/libdrmaa.so.1.0
However I can't locate the the file libdrmaa.so.1.0.3 anywhere. In fact I don't have have an lsf nor sge directory within galaxy-dist.
Thanks,
Greg
___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
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On Nov 5, 2012, at 3:40 PM, greg wrote:
Ok, that makes sense.
Would you mind sharing how you set up your init script?
What goes in it, where you place it?
There are some sample init scripts in the contrib/ directory of the distribution. You should be able to place the export near the top, where other variables are set. --nate
Thanks again,
Greg
On Mon, Nov 5, 2012 at 3:33 PM, Nate Coraor <nate@bx.psu.edu> wrote:
On Nov 5, 2012, at 3:26 PM, greg wrote:
Well, I want it to ultimately run under Apache. Does it still make sense to go in an init script?
thanks again,
Yes, even when running behind Apache, you'll need an init script (or similar method) to start the Galaxy server.
--nate
Greg
On Mon, Nov 5, 2012 at 3:23 PM, Nate Coraor <nate@bx.psu.edu> wrote:
On Nov 5, 2012, at 3:15 PM, greg wrote:
And am I correct in the thinking that only the machine hosting the galaxy web interface and submitting jobs needs the export DRMAA_LIBRARY_PATH= variable?
The normal nodes running jobs don't need this, right?
Hi Greg,
That's correct. If you're starting Galaxy with an init script, I'd put the export there.
--nate
Thanks,
-Greg
On Mon, Nov 5, 2012 at 3:12 PM, greg <margeemail@gmail.com> wrote:
Thanks Scott. I did turn up: /sge/8.0.1p4/lib/lx-amd64/libdrmaa.so.1.0
I guess that would be it.
For a followup question ,how do I make the DRMAA_LIBRARY_PATH variable permanent on the machine?
-Greg
On Mon, Nov 5, 2012 at 3:03 PM, Scott McManus <scottmcmanus@gatech.edu> wrote: > > I forgot to add my value of DRMAA_LIBRARY_PATH. Note that I just need > DRMAA_LIBRARY_PATH to point to the library being used. So in the example > below, I had this: > >> echo $DRMAA_LIBRARY_PATH > /usr/lib/libdrmaa.so > > -Scott > > ________________________________ > > Have you installed SGE on the same machine? If so, then you should be able > to > do a "locate libdrmaa.so", which should point to SGE's DRMAA library. For > example, > on a machine that I use, I see this: > > $ locate libdrmaa.so > /usr/lib/libdrmaa.so > /usr/lib/libdrmaa.so.1.0 > $ ls /usr/lib/libdrmaa* > /usr/lib/libdrmaa.so /usr/lib/libdrmaa.so.1.0 > $ ls -la /usr/lib/libdrmaa.so > lrwxrwxrwx 1 root root 15 Apr 18 2012 /usr/lib/libdrmaa.so -> > libdrmaa.so.1.0 > > You may also want to try "updatedb" (again, assuming you're using Linux) > to index > the files on your machine. Finally, if you can't find it, then you should > check if you > actually have SGE installed on that machine. I like to use "dpkg" on > Ubuntu/Debian > and "yum" on Centos to manipulate packages. > > -Scott > > ________________________________ > > I'm trying to install Galaxy on our SGE cluster (using the Unified > method). > > I installed galaxy-dist, and now I'm on this section: > > drmaa egg > > The drmaa egg is provided by Galaxy, but you must tell it where your > resource manager's DRMAA library is located, and this is done with > the$DRMAA_LIBRARY_PATH environment variable: > > % export > DRMAA_LIBRARY_PATH=/galaxy/lsf/7.0/linux2.6-glibc2.3-x86_64/lib/libdrmaa.so.1.0.3 > % export DRMAA_LIBRARY_PATH=/galaxy/sge/lib/lx24-amd64/libdrmaa.so.1.0 > > > However I can't locate the the file libdrmaa.so.1.0.3 anywhere. In fact I > don't have have an lsf nor sge directory within galaxy-dist. > > Thanks, > > Greg > > ___________________________________________________________ > The Galaxy User list should be used for the discussion of > Galaxy analysis and other features on the public server > at usegalaxy.org. Please keep all replies on the list by > using "reply all" in your mail client. For discussion of > local Galaxy instances and the Galaxy source code, please > use the Galaxy Development list: > > http://lists.bx.psu.edu/listinfo/galaxy-dev > > To manage your subscriptions to this and other Galaxy lists, > please use the interface at: > > http://lists.bx.psu.edu/ > > > > ___________________________________________________________ > The Galaxy User list should be used for the discussion of > Galaxy analysis and other features on the public server > at usegalaxy.org. Please keep all replies on the list by > using "reply all" in your mail client. For discussion of > local Galaxy instances and the Galaxy source code, please > use the Galaxy Development list: > > http://lists.bx.psu.edu/listinfo/galaxy-dev > > To manage your subscriptions to this and other Galaxy lists, > please use the interface at: > > http://lists.bx.psu.edu/ > >
___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
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On Nov 5, 2012, at 3:40 PM, greg <margeemail@gmail.com> wrote:
Ok, that makes sense.
Would you mind sharing how you set up your init script?
What goes in it, where you place it?
Thanks again,
Greg
You can just start a screen session on the head node, cd into the galaxy directory and run "sh run.sh --reload" to start the processes or write a script to handle Galaxy in the daemon mode at any degree of granularity. For instance, here is my shell script that I use to start/stop/restart manager/runner, web runners or everything together as needed: http://pastie.org/5191826 Regards, Alex
participants (4)
-
greg -
Nate Coraor -
Oleksandr Moskalenko -
Scott McManus