Galaxy CloudMan - Nodes can't make their own qsub calls?
Hi guys, I created a new Galaxy instance web launcher (https://biocloudcentral.herokuapp.com/launch) and then I ssh'd into the master node. I'm trying to run a Perl script that makes several qsub calls to other perl scripts. Now the catch is that one of those perl scripts makes its own qsub calls. And I'm getting this error when it tries to do that: Unable to run job: denied: host "ip-10-29-176-111.ec2.internal" is no submit host. Somehow this works fine on other clusters I've run this code on. Any idea what could be going on? Do I need to make all of the nodes "submit hosts"? Thanks a bunch! -Greg
As a follow up I found a command that should add the new nodes as submit hosts and I tried to run it but I got this error: $ qconf -as ip-10-28-164-178.ec2.internal denied: "ubuntu" must be manager for this operation What does it mean by manager? How would I run this command? I guess my preference is for Cloudman to do this automatically though so I'll be distributing this program to 3rd party users using the built-in cloudman sharing. I can't rightly ask users to be running qconf. Thanks again, Greg On Thu, Sep 13, 2012 at 3:59 PM, greg <margeemail@gmail.com> wrote:
Hi guys,
I created a new Galaxy instance web launcher (https://biocloudcentral.herokuapp.com/launch) and then I ssh'd into the master node.
I'm trying to run a Perl script that makes several qsub calls to other perl scripts. Now the catch is that one of those perl scripts makes its own qsub calls.
And I'm getting this error when it tries to do that:
Unable to run job: denied: host "ip-10-29-176-111.ec2.internal" is no submit host.
Somehow this works fine on other clusters I've run this code on. Any idea what could be going on? Do I need to make all of the nodes "submit hosts"?
Thanks a bunch!
-Greg
You probably need to sudo to sgeadmin (cloudman guys correct me if you have this setup differently). I don't see any reason not to make worker nodes submit hosts by default in a future cloudman release. -- jt On Thu, Sep 13, 2012 at 4:17 PM, greg <margeemail@gmail.com> wrote:
As a follow up I found a command that should add the new nodes as submit hosts and I tried to run it but I got this error:
$ qconf -as ip-10-28-164-178.ec2.internal denied: "ubuntu" must be manager for this operation
What does it mean by manager? How would I run this command?
I guess my preference is for Cloudman to do this automatically though so I'll be distributing this program to 3rd party users using the built-in cloudman sharing. I can't rightly ask users to be running qconf.
Thanks again,
Greg
On Thu, Sep 13, 2012 at 3:59 PM, greg <margeemail@gmail.com> wrote:
Hi guys,
I created a new Galaxy instance web launcher (https://biocloudcentral.herokuapp.com/launch) and then I ssh'd into the master node.
I'm trying to run a Perl script that makes several qsub calls to other perl scripts. Now the catch is that one of those perl scripts makes its own qsub calls.
And I'm getting this error when it tries to do that:
Unable to run job: denied: host "ip-10-29-176-111.ec2.internal" is no submit host.
Somehow this works fine on other clusters I've run this code on. Any idea what could be going on? Do I need to make all of the nodes "submit hosts"?
Thanks a bunch!
-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:
Thanks James. I'll give that a try. That would be excellent if you could make work nodes submit hosts by default in a future release. How would I get that on the plans? Submit a ticket somewhere? I guess in the meantime I could write a python script that runs qconf -sconfl to list all the hosts and for any that aren't listed when running qconf -ss, it would run qconf -as hostname on them. -Greg On Thu, Sep 13, 2012 at 5:00 PM, James Taylor <james@jamestaylor.org> wrote:
You probably need to sudo to sgeadmin (cloudman guys correct me if you have this setup differently).
I don't see any reason not to make worker nodes submit hosts by default in a future cloudman release.
-- jt
On Thu, Sep 13, 2012 at 4:17 PM, greg <margeemail@gmail.com> wrote:
As a follow up I found a command that should add the new nodes as submit hosts and I tried to run it but I got this error:
$ qconf -as ip-10-28-164-178.ec2.internal denied: "ubuntu" must be manager for this operation
What does it mean by manager? How would I run this command?
I guess my preference is for Cloudman to do this automatically though so I'll be distributing this program to 3rd party users using the built-in cloudman sharing. I can't rightly ask users to be running qconf.
Thanks again,
Greg
On Thu, Sep 13, 2012 at 3:59 PM, greg <margeemail@gmail.com> wrote:
Hi guys,
I created a new Galaxy instance web launcher (https://biocloudcentral.herokuapp.com/launch) and then I ssh'd into the master node.
I'm trying to run a Perl script that makes several qsub calls to other perl scripts. Now the catch is that one of those perl scripts makes its own qsub calls.
And I'm getting this error when it tries to do that:
Unable to run job: denied: host "ip-10-29-176-111.ec2.internal" is no submit host.
Somehow this works fine on other clusters I've run this code on. Any idea what could be going on? Do I need to make all of the nodes "submit hosts"?
Thanks a bunch!
-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:
Ok, here's what I tried: $ sudo -u sgeadmin qconf -as ip-10-29-213-80.ec2.internal sudo: qconf: command not found So then I tried: $ which qconf /opt/sge/bin/lx24-amd64/qconf $ sudo -u sgeadmin /opt/sge/bin/lx24-amd64/qconf -as ip-10-29-213-80.ec2.internal critical error: Please set the environment variable SGE_ROOT. So then I tried: $ echo $SGE_ROOT /opt/sge $ sudo -u sgeadmin export SGE_ROOT=/opt/sge sudo: export: command not found Any ideas? I don't have the greatest understanding of the export command. Thanks again, Greg On Fri, Sep 14, 2012 at 8:23 AM, greg <margeemail@gmail.com> wrote:
Thanks James. I'll give that a try. That would be excellent if you could make work nodes submit hosts by default in a future release. How would I get that on the plans? Submit a ticket somewhere?
I guess in the meantime I could write a python script that runs qconf -sconfl to list all the hosts and for any that aren't listed when running qconf -ss, it would run qconf -as hostname on them.
-Greg
On Thu, Sep 13, 2012 at 5:00 PM, James Taylor <james@jamestaylor.org> wrote:
You probably need to sudo to sgeadmin (cloudman guys correct me if you have this setup differently).
I don't see any reason not to make worker nodes submit hosts by default in a future cloudman release.
-- jt
On Thu, Sep 13, 2012 at 4:17 PM, greg <margeemail@gmail.com> wrote:
As a follow up I found a command that should add the new nodes as submit hosts and I tried to run it but I got this error:
$ qconf -as ip-10-28-164-178.ec2.internal denied: "ubuntu" must be manager for this operation
What does it mean by manager? How would I run this command?
I guess my preference is for Cloudman to do this automatically though so I'll be distributing this program to 3rd party users using the built-in cloudman sharing. I can't rightly ask users to be running qconf.
Thanks again,
Greg
On Thu, Sep 13, 2012 at 3:59 PM, greg <margeemail@gmail.com> wrote:
Hi guys,
I created a new Galaxy instance web launcher (https://biocloudcentral.herokuapp.com/launch) and then I ssh'd into the master node.
I'm trying to run a Perl script that makes several qsub calls to other perl scripts. Now the catch is that one of those perl scripts makes its own qsub calls.
And I'm getting this error when it tries to do that:
Unable to run job: denied: host "ip-10-29-176-111.ec2.internal" is no submit host.
Somehow this works fine on other clusters I've run this code on. Any idea what could be going on? Do I need to make all of the nodes "submit hosts"?
Thanks a bunch!
-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:
Spoke too soon! $ sudo -E -u sgeadmin /opt/sge/bin/lx24-amd64/qconf -as ip-10-29-213-80.ec2.internal worked fine. -E tells sudo to use the users environment. -Greg On Fri, Sep 14, 2012 at 2:24 PM, greg <margeemail@gmail.com> wrote:
Ok, here's what I tried:
$ sudo -u sgeadmin qconf -as ip-10-29-213-80.ec2.internal sudo: qconf: command not found
So then I tried:
$ which qconf /opt/sge/bin/lx24-amd64/qconf $ sudo -u sgeadmin /opt/sge/bin/lx24-amd64/qconf -as ip-10-29-213-80.ec2.internal critical error: Please set the environment variable SGE_ROOT.
So then I tried:
$ echo $SGE_ROOT /opt/sge $ sudo -u sgeadmin export SGE_ROOT=/opt/sge sudo: export: command not found
Any ideas? I don't have the greatest understanding of the export command.
Thanks again,
Greg
On Fri, Sep 14, 2012 at 8:23 AM, greg <margeemail@gmail.com> wrote:
Thanks James. I'll give that a try. That would be excellent if you could make work nodes submit hosts by default in a future release. How would I get that on the plans? Submit a ticket somewhere?
I guess in the meantime I could write a python script that runs qconf -sconfl to list all the hosts and for any that aren't listed when running qconf -ss, it would run qconf -as hostname on them.
-Greg
On Thu, Sep 13, 2012 at 5:00 PM, James Taylor <james@jamestaylor.org> wrote:
You probably need to sudo to sgeadmin (cloudman guys correct me if you have this setup differently).
I don't see any reason not to make worker nodes submit hosts by default in a future cloudman release.
-- jt
On Thu, Sep 13, 2012 at 4:17 PM, greg <margeemail@gmail.com> wrote:
As a follow up I found a command that should add the new nodes as submit hosts and I tried to run it but I got this error:
$ qconf -as ip-10-28-164-178.ec2.internal denied: "ubuntu" must be manager for this operation
What does it mean by manager? How would I run this command?
I guess my preference is for Cloudman to do this automatically though so I'll be distributing this program to 3rd party users using the built-in cloudman sharing. I can't rightly ask users to be running qconf.
Thanks again,
Greg
On Thu, Sep 13, 2012 at 3:59 PM, greg <margeemail@gmail.com> wrote:
Hi guys,
I created a new Galaxy instance web launcher (https://biocloudcentral.herokuapp.com/launch) and then I ssh'd into the master node.
I'm trying to run a Perl script that makes several qsub calls to other perl scripts. Now the catch is that one of those perl scripts makes its own qsub calls.
And I'm getting this error when it tries to do that:
Unable to run job: denied: host "ip-10-29-176-111.ec2.internal" is no submit host.
Somehow this works fine on other clusters I've run this code on. Any idea what could be going on? Do I need to make all of the nodes "submit hosts"?
Thanks a bunch!
-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:
Hey all, Here's the one-liner I came up with for my users to run until this is changed in Galaxy: $ qconf -sconfl | xargs -l sudo -E -u sgeadmin /opt/sge/bin/lx24-amd64/qconf -as (in case anyone is interested) -Greg On Fri, Sep 14, 2012 at 2:27 PM, greg <margeemail@gmail.com> wrote:
Spoke too soon!
$ sudo -E -u sgeadmin /opt/sge/bin/lx24-amd64/qconf -as ip-10-29-213-80.ec2.internal
worked fine. -E tells sudo to use the users environment.
-Greg
On Fri, Sep 14, 2012 at 2:24 PM, greg <margeemail@gmail.com> wrote:
Ok, here's what I tried:
$ sudo -u sgeadmin qconf -as ip-10-29-213-80.ec2.internal sudo: qconf: command not found
So then I tried:
$ which qconf /opt/sge/bin/lx24-amd64/qconf $ sudo -u sgeadmin /opt/sge/bin/lx24-amd64/qconf -as ip-10-29-213-80.ec2.internal critical error: Please set the environment variable SGE_ROOT.
So then I tried:
$ echo $SGE_ROOT /opt/sge $ sudo -u sgeadmin export SGE_ROOT=/opt/sge sudo: export: command not found
Any ideas? I don't have the greatest understanding of the export command.
Thanks again,
Greg
On Fri, Sep 14, 2012 at 8:23 AM, greg <margeemail@gmail.com> wrote:
Thanks James. I'll give that a try. That would be excellent if you could make work nodes submit hosts by default in a future release. How would I get that on the plans? Submit a ticket somewhere?
I guess in the meantime I could write a python script that runs qconf -sconfl to list all the hosts and for any that aren't listed when running qconf -ss, it would run qconf -as hostname on them.
-Greg
On Thu, Sep 13, 2012 at 5:00 PM, James Taylor <james@jamestaylor.org> wrote:
You probably need to sudo to sgeadmin (cloudman guys correct me if you have this setup differently).
I don't see any reason not to make worker nodes submit hosts by default in a future cloudman release.
-- jt
On Thu, Sep 13, 2012 at 4:17 PM, greg <margeemail@gmail.com> wrote:
As a follow up I found a command that should add the new nodes as submit hosts and I tried to run it but I got this error:
$ qconf -as ip-10-28-164-178.ec2.internal denied: "ubuntu" must be manager for this operation
What does it mean by manager? How would I run this command?
I guess my preference is for Cloudman to do this automatically though so I'll be distributing this program to 3rd party users using the built-in cloudman sharing. I can't rightly ask users to be running qconf.
Thanks again,
Greg
On Thu, Sep 13, 2012 at 3:59 PM, greg <margeemail@gmail.com> wrote:
Hi guys,
I created a new Galaxy instance web launcher (https://biocloudcentral.herokuapp.com/launch) and then I ssh'd into the master node.
I'm trying to run a Perl script that makes several qsub calls to other perl scripts. Now the catch is that one of those perl scripts makes its own qsub calls.
And I'm getting this error when it tries to do that:
Unable to run job: denied: host "ip-10-29-176-111.ec2.internal" is no submit host.
Somehow this works fine on other clusters I've run this code on. Any idea what could be going on? Do I need to make all of the nodes "submit hosts"?
Thanks a bunch!
-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:
Added: worker nodes are now submit hosts as well: https://bitbucket.org/galaxy/cloudman/changeset/b4c66783b42fb559b35b689363b3... This will be generally available with the next release of CloudMan is made (however, there is no immediate plans for doing so as quite a bit of other details need to ironed out before the code is stable). On Sat, Sep 15, 2012 at 4:36 AM, greg <margeemail@gmail.com> wrote:
Hey all,
Here's the one-liner I came up with for my users to run until this is changed in Galaxy:
$ qconf -sconfl | xargs -l sudo -E -u sgeadmin /opt/sge/bin/lx24-amd64/qconf -as
(in case anyone is interested)
-Greg
On Fri, Sep 14, 2012 at 2:27 PM, greg <margeemail@gmail.com> wrote:
Spoke too soon!
$ sudo -E -u sgeadmin /opt/sge/bin/lx24-amd64/qconf -as ip-10-29-213-80.ec2.internal
worked fine. -E tells sudo to use the users environment.
-Greg
On Fri, Sep 14, 2012 at 2:24 PM, greg <margeemail@gmail.com> wrote:
Ok, here's what I tried:
$ sudo -u sgeadmin qconf -as ip-10-29-213-80.ec2.internal sudo: qconf: command not found
So then I tried:
$ which qconf /opt/sge/bin/lx24-amd64/qconf $ sudo -u sgeadmin /opt/sge/bin/lx24-amd64/qconf -as ip-10-29-213-80.ec2.internal critical error: Please set the environment variable SGE_ROOT.
So then I tried:
$ echo $SGE_ROOT /opt/sge $ sudo -u sgeadmin export SGE_ROOT=/opt/sge sudo: export: command not found
Any ideas? I don't have the greatest understanding of the export command.
Thanks again,
Greg
On Fri, Sep 14, 2012 at 8:23 AM, greg <margeemail@gmail.com> wrote:
Thanks James. I'll give that a try. That would be excellent if you could make work nodes submit hosts by default in a future release. How would I get that on the plans? Submit a ticket somewhere?
I guess in the meantime I could write a python script that runs qconf -sconfl to list all the hosts and for any that aren't listed when running qconf -ss, it would run qconf -as hostname on them.
-Greg
On Thu, Sep 13, 2012 at 5:00 PM, James Taylor <james@jamestaylor.org> wrote:
You probably need to sudo to sgeadmin (cloudman guys correct me if you have this setup differently).
I don't see any reason not to make worker nodes submit hosts by default in a future cloudman release.
-- jt
On Thu, Sep 13, 2012 at 4:17 PM, greg <margeemail@gmail.com> wrote:
As a follow up I found a command that should add the new nodes as submit hosts and I tried to run it but I got this error:
$ qconf -as ip-10-28-164-178.ec2.internal denied: "ubuntu" must be manager for this operation
What does it mean by manager? How would I run this command?
I guess my preference is for Cloudman to do this automatically though so I'll be distributing this program to 3rd party users using the built-in cloudman sharing. I can't rightly ask users to be running qconf.
Thanks again,
Greg
On Thu, Sep 13, 2012 at 3:59 PM, greg <margeemail@gmail.com> wrote: > Hi guys, > > I created a new Galaxy instance web launcher > (https://biocloudcentral.herokuapp.com/launch) and then I ssh'd into > the master node. > > I'm trying to run a Perl script that makes several qsub calls to other > perl scripts. Now the catch is that one of those perl scripts makes > its own qsub calls. > > And I'm getting this error when it tries to do that: > > Unable to run job: denied: host "ip-10-29-176-111.ec2.internal" is no > submit host. > > > Somehow this works fine on other clusters I've run this code on. Any > idea what could be going on? Do I need to make all of the nodes > "submit hosts"? > > Thanks a bunch! > > -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:
Thanks Enis. You guys are fast! Feel free to pass on my one-liner if anyone needs this before the next release. -Greg On Sat, Sep 15, 2012 at 8:26 PM, Enis Afgan <eafgan@emory.edu> wrote:
Added: worker nodes are now submit hosts as well: https://bitbucket.org/galaxy/cloudman/changeset/b4c66783b42fb559b35b689363b3...
This will be generally available with the next release of CloudMan is made (however, there is no immediate plans for doing so as quite a bit of other details need to ironed out before the code is stable).
On Sat, Sep 15, 2012 at 4:36 AM, greg <margeemail@gmail.com> wrote:
Hey all,
Here's the one-liner I came up with for my users to run until this is changed in Galaxy:
$ qconf -sconfl | xargs -l sudo -E -u sgeadmin /opt/sge/bin/lx24-amd64/qconf -as
(in case anyone is interested)
-Greg
On Fri, Sep 14, 2012 at 2:27 PM, greg <margeemail@gmail.com> wrote:
Spoke too soon!
$ sudo -E -u sgeadmin /opt/sge/bin/lx24-amd64/qconf -as ip-10-29-213-80.ec2.internal
worked fine. -E tells sudo to use the users environment.
-Greg
On Fri, Sep 14, 2012 at 2:24 PM, greg <margeemail@gmail.com> wrote:
Ok, here's what I tried:
$ sudo -u sgeadmin qconf -as ip-10-29-213-80.ec2.internal sudo: qconf: command not found
So then I tried:
$ which qconf /opt/sge/bin/lx24-amd64/qconf $ sudo -u sgeadmin /opt/sge/bin/lx24-amd64/qconf -as ip-10-29-213-80.ec2.internal critical error: Please set the environment variable SGE_ROOT.
So then I tried:
$ echo $SGE_ROOT /opt/sge $ sudo -u sgeadmin export SGE_ROOT=/opt/sge sudo: export: command not found
Any ideas? I don't have the greatest understanding of the export command.
Thanks again,
Greg
On Fri, Sep 14, 2012 at 8:23 AM, greg <margeemail@gmail.com> wrote:
Thanks James. I'll give that a try. That would be excellent if you could make work nodes submit hosts by default in a future release. How would I get that on the plans? Submit a ticket somewhere?
I guess in the meantime I could write a python script that runs qconf -sconfl to list all the hosts and for any that aren't listed when running qconf -ss, it would run qconf -as hostname on them.
-Greg
On Thu, Sep 13, 2012 at 5:00 PM, James Taylor <james@jamestaylor.org> wrote:
You probably need to sudo to sgeadmin (cloudman guys correct me if you have this setup differently).
I don't see any reason not to make worker nodes submit hosts by default in a future cloudman release.
-- jt
On Thu, Sep 13, 2012 at 4:17 PM, greg <margeemail@gmail.com> wrote: > As a follow up I found a command that should add the new nodes as > submit hosts and I tried to run it but I got this error: > > $ qconf -as ip-10-28-164-178.ec2.internal > denied: "ubuntu" must be manager for this operation > > What does it mean by manager? How would I run this command? > > > I guess my preference is for Cloudman to do this automatically > though > so I'll be distributing this program to 3rd party users using the > built-in cloudman sharing. I can't rightly ask users to be running > qconf. > > Thanks again, > > Greg > > > On Thu, Sep 13, 2012 at 3:59 PM, greg <margeemail@gmail.com> wrote: >> Hi guys, >> >> I created a new Galaxy instance web launcher >> (https://biocloudcentral.herokuapp.com/launch) and then I ssh'd >> into >> the master node. >> >> I'm trying to run a Perl script that makes several qsub calls to >> other >> perl scripts. Now the catch is that one of those perl scripts >> makes >> its own qsub calls. >> >> And I'm getting this error when it tries to do that: >> >> Unable to run job: denied: host "ip-10-29-176-111.ec2.internal" is >> no >> submit host. >> >> >> Somehow this works fine on other clusters I've run this code on. >> Any >> idea what could be going on? Do I need to make all of the nodes >> "submit hosts"? >> >> Thanks a bunch! >> >> -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:
participants (3)
-
Enis Afgan -
greg -
James Taylor