-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1
This is specifically to galaxy administrators and developers who have worked with galaxy and cluster deployment.
If you have successfully deployed a galaxy instance backed by one (or more) clusters, I'm looking to hear about your experience;
- - the configuration - - any pitfalls encountered - - any extra tools that needed to be installed - - any ugly hacks you had to implement
The current cluster documentation is somewhat lacking, and I'm willing to compile everyone's experiences deploying to clusters if you're willing to send them in. I'll update the cluster page on the wiki as I receive replies and can allocate time.
By way of example, here's the summary of what I would reply to this email with my experiences deploying to an HTCondor cluster
- - HTcondor ran fine, accepted jobs and worked for all users - - Connecting galaxy to it would result in some jobs running/some jobs failing. It was determined that those jobs which ran, were only on localhost. - - This was a result of the fact that galaxy's home directory/data was not exported - - Galaxy was made an LDAP user and a folder created in the correct location on all computers - - This still failed, as galaxy does not transfer files by default (as far as I can tell), even though that's available in HTCondor - - Finally galaxy's home directory was NFS exported and things seemed to work.
Cheers, Eric
- -- Eric Rasche Programmer II Center for Phage Technology Texas A&M University College Station, TX 77843 404-692-2048 esr@tamu.edu rasche.eric@yandex.ru
Hi Eric,
thanks for caring about that issue.
Do you know about Galaxy Community Hubs?
https://wiki.galaxyproject.org/Community/
The community is encouraged to share experience under that page. Maybe you can add yours to that page as well?
Cheers, Bjoern
Am 27.05.2014 18:32, schrieb Eric Rasche:
-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1
This is specifically to galaxy administrators and developers who have worked with galaxy and cluster deployment.
If you have successfully deployed a galaxy instance backed by one (or more) clusters, I'm looking to hear about your experience;
- the configuration
- any pitfalls encountered
- any extra tools that needed to be installed
- any ugly hacks you had to implement
The current cluster documentation is somewhat lacking, and I'm willing to compile everyone's experiences deploying to clusters if you're willing to send them in. I'll update the cluster page on the wiki as I receive replies and can allocate time.
By way of example, here's the summary of what I would reply to this email with my experiences deploying to an HTCondor cluster
- HTcondor ran fine, accepted jobs and worked for all users
- Connecting galaxy to it would result in some jobs running/some jobs
failing. It was determined that those jobs which ran, were only on localhost.
- This was a result of the fact that galaxy's home directory/data was
not exported
- Galaxy was made an LDAP user and a folder created in the correct
location on all computers
- This still failed, as galaxy does not transfer files by default (as
far as I can tell), even though that's available in HTCondor
- Finally galaxy's home directory was NFS exported and things seemed to
work.
Cheers, Eric
Eric Rasche Programmer II Center for Phage Technology Texas A&M University College Station, TX 77843 404-692-2048 esr@tamu.edu rasche.eric@yandex.ru -----BEGIN PGP SIGNATURE----- Version: GnuPG v2.0.17 (GNU/Linux)
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To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1
Hi Bjoern,
Yes, I am aware of such. I had intended to update the Cluster docs as it's the more appropriate page, perhaps linking to it from the community log page.
I was hoping that people might send in their experiences so I could aggregate them and write the entries for them. There's always a lot of apathy towards documentation, and given that this is a feature used by a select few (even if many organisations use it, only a handful of people are actually doing the deployment), I figured that they might be more easily convinced to simply summarise their issues/experiences in a dozen bulletpoints. Additionally by aggregation we could easily identify common problems and highlight those for others to see.
That said...no one has replied to this yet. I fully intend to at least include mine, however I was holding out for some other replies.
Cheers, Eric
On 06/02/2014 08:55 AM, Björn Grüning wrote:
Hi Eric,
thanks for caring about that issue.
Do you know about Galaxy Community Hubs?
https://wiki.galaxyproject.org/Community/
The community is encouraged to share experience under that page. Maybe
you can add yours to that page as well?
Cheers, Bjoern
Am 27.05.2014 18:32, schrieb Eric Rasche: This is specifically to galaxy administrators and developers who have worked with galaxy and cluster deployment.
If you have successfully deployed a galaxy instance backed by one (or more) clusters, I'm looking to hear about your experience;
- the configuration
- any pitfalls encountered
- any extra tools that needed to be installed
- any ugly hacks you had to implement
The current cluster documentation is somewhat lacking, and I'm willing to compile everyone's experiences deploying to clusters if you're willing to send them in. I'll update the cluster page on the wiki as I receive replies and can allocate time.
By way of example, here's the summary of what I would reply to this email with my experiences deploying to an HTCondor cluster
- HTcondor ran fine, accepted jobs and worked for all users
- Connecting galaxy to it would result in some jobs running/some jobs
failing. It was determined that those jobs which ran, were only on localhost.
- This was a result of the fact that galaxy's home directory/data was
not exported
- Galaxy was made an LDAP user and a folder created in the correct
location on all computers
- This still failed, as galaxy does not transfer files by default (as
far as I can tell), even though that's available in HTCondor
- Finally galaxy's home directory was NFS exported and things seemed to
work.
Cheers, Eric
Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
- -- Eric Rasche Programmer II Center for Phage Technology Texas A&M University College Station, TX 77843
Hi,
Yes, I am aware of such. I had intended to update the Cluster docs as it's the more appropriate page, perhaps linking to it from the community log page.
I was hoping that people might send in their experiences so I could aggregate them and write the entries for them. There's always a lot of apathy towards documentation, and given that this is a feature used by a select few (even if many organisations use it, only a handful of people are actually doing the deployment), I figured that they might be more easily convinced to simply summarise their issues/experiences in a dozen bulletpoints. Additionally by aggregation we could easily identify common problems and highlight those for others to see.
That is always good, yes, but hard to motivate people. My problem is that I do not remember every detail of every problem, it's to far away. Galaxy is running for us now. But if I encounter any new problem I will let you and the wiki know.
That said...no one has replied to this yet. I fully intend to at least include mine, however I was holding out for some other replies.
Fingers crossed! Bjoern
Cheers, Eric
On 06/02/2014 08:55 AM, Björn Grüning wrote:
Hi Eric,
thanks for caring about that issue.
Do you know about Galaxy Community Hubs?
https://wiki.galaxyproject.org/Community/
The community is encouraged to share experience under that page. Maybe
you can add yours to that page as well?
Cheers, Bjoern
Am 27.05.2014 18:32, schrieb Eric Rasche: This is specifically to galaxy administrators and developers who have worked with galaxy and cluster deployment.
If you have successfully deployed a galaxy instance backed by one (or more) clusters, I'm looking to hear about your experience;
- the configuration
- any pitfalls encountered
- any extra tools that needed to be installed
- any ugly hacks you had to implement
The current cluster documentation is somewhat lacking, and I'm willing to compile everyone's experiences deploying to clusters if you're willing to send them in. I'll update the cluster page on the wiki as I receive replies and can allocate time.
By way of example, here's the summary of what I would reply to this email with my experiences deploying to an HTCondor cluster
- HTcondor ran fine, accepted jobs and worked for all users
- Connecting galaxy to it would result in some jobs running/some jobs
failing. It was determined that those jobs which ran, were only on localhost.
- This was a result of the fact that galaxy's home directory/data was
not exported
- Galaxy was made an LDAP user and a folder created in the correct
location on all computers
- This still failed, as galaxy does not transfer files by default (as
far as I can tell), even though that's available in HTCondor
- Finally galaxy's home directory was NFS exported and things seemed to
work.
Cheers, Eric
Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Eric Rasche Programmer II Center for Phage Technology Texas A&M University College Station, TX 77843 -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.11 (GNU/Linux) Comment: Using GnuPG with Thunderbird - http://www.enigmail.net/
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galaxy-dev@lists.galaxyproject.org
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Björn Grüning -
Eric Rasche