Re: [galaxy-dev] how to use projects for fair-share on compute-cluster
Sure, it's on the todo list. Ping me again in a year. ;)
--nate
On Jan 20, 2012, at 7:33 PM, Edward Kirton wrote:
Great idea, Nate (hint! hint!).
On Thu, Jan 19, 2012 at 10:27 AM, Nate Coraor n...@bx.psu.edu wrote:
Hey Ed,
This is a neat approach. You could possibly also do this in the Galaxy
database by associating users and groups with roles that match project
names. A select list or history default that allowed users to select their
current project/role would remove the single-project-per-user limitation.
--nate
On Jan 13, 2012, at 3:17 PM, Edward Kirton wrote:
correction: i didn't adequately test what happens if the user_proj_map_db
was not defined in the universe file; here's the changes:
157 # BEGIN ADD USER'S PROJ
158 try:
159 conn = sqlite3.connect(self.app.config.user_proj_map_db)
160 c = conn.cursor()
161 c.execute('SELECT PROJ FROM USER_PROJ WHERE GID=?',
[job_wrapper.user_id])
162 row = c.fetchone()
163 c.close
164 native_spec += ' -P ' + row[0]
165 except:
166 log.debug(Cannot look up proj of user %s %
job_wrapper.user_id)
167 # /END ADD USER PROJ
also, in the config, define a default instead of using None:
self.user_proj_map_db = resolve_path( kwargs.get(
user_proj_map_db, database/user_proj_map.sqlite ), self.root )
one last note: there doesn't seem to be any error displayed to the user if
the job cannot be scheduled because the galaxy user doesn't have
permissions to use the user's project (although there is a log entry), but
the job will never be scheduled. so be sure the galaxy user has
permissions to submit to all possible projects.
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Re: [galaxy-dev] how to use projects for fair-share on compute-cluster
Great idea, Nate (hint! hint!).
On Thu, Jan 19, 2012 at 10:27 AM, Nate Coraor n...@bx.psu.edu wrote:
Hey Ed,
This is a neat approach. You could possibly also do this in the Galaxy
database by associating users and groups with roles that match project names.
A select list or history default that allowed users to select their
current project/role would remove the single-project-per-user limitation.
--nate
On Jan 13, 2012, at 3:17 PM, Edward Kirton wrote:
correction: i didn't adequately test what happens if the user_proj_map_db
was not defined in the universe file; here's the changes:
157 # BEGIN ADD USER'S PROJ
158 try:
159 conn = sqlite3.connect(self.app.config.user_proj_map_db)
160 c = conn.cursor()
161 c.execute('SELECT PROJ FROM USER_PROJ WHERE GID=?',
[job_wrapper.user_id])
162 row = c.fetchone()
163 c.close
164 native_spec += ' -P ' + row[0]
165 except:
166 log.debug(Cannot look up proj of user %s %
job_wrapper.user_id)
167 # /END ADD USER PROJ
also, in the config, define a default instead of using None:
self.user_proj_map_db = resolve_path( kwargs.get(
user_proj_map_db, database/user_proj_map.sqlite ), self.root )
one last note: there doesn't seem to be any error displayed to the user if
the job cannot be scheduled because the galaxy user doesn't have permissions
to use the user's project (although there is a log entry), but the job will
never be scheduled. so be sure the galaxy user has permissions to submit to
all possible projects.
___
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/
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Please keep all replies on the list by using reply all
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Re: [galaxy-dev] how to use projects for fair-share on compute-cluster
I really want this for Torque/Moab where the native spec flag is -A
Sent from my iPhone
On Jan 20, 2012, at 7:34 PM, Edward Kirton eskir...@lbl.gov wrote:
Great idea, Nate (hint! hint!).
On Thu, Jan 19, 2012 at 10:27 AM, Nate Coraor n...@bx.psu.edu wrote:
Hey Ed,
This is a neat approach. You could possibly also do this in the Galaxy
database by associating users and groups with roles that match project
names. A select list or history default that allowed users to select their
current project/role would remove the single-project-per-user limitation.
--nate
On Jan 13, 2012, at 3:17 PM, Edward Kirton wrote:
correction: i didn't adequately test what happens if the user_proj_map_db
was not defined in the universe file; here's the changes:
157 # BEGIN ADD USER'S PROJ
158 try:
159 conn = sqlite3.connect(self.app.config.user_proj_map_db)
160 c = conn.cursor()
161 c.execute('SELECT PROJ FROM USER_PROJ WHERE GID=?',
[job_wrapper.user_id])
162 row = c.fetchone()
163 c.close
164 native_spec += ' -P ' + row[0]
165 except:
166 log.debug(Cannot look up proj of user %s %
job_wrapper.user_id)
167 # /END ADD USER PROJ
also, in the config, define a default instead of using None:
self.user_proj_map_db = resolve_path( kwargs.get(
user_proj_map_db, database/user_proj_map.sqlite ), self.root )
one last note: there doesn't seem to be any error displayed to the user if
the job cannot be scheduled because the galaxy user doesn't have
permissions to use the user's project (although there is a log entry), but
the job will never be scheduled. so be sure the galaxy user has
permissions to submit to all possible projects.
___
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/
___
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/
___
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/
Re: [galaxy-dev] how to use projects for fair-share on compute-cluster
correction: i didn't adequately test what happens if the user_proj_map_db
was not defined in the universe file; here's the changes:
157 # BEGIN ADD USER'S PROJ
158 try:
159 conn = sqlite3.connect(self.app.config.user_proj_map_db)
160 c = conn.cursor()
161 c.execute('SELECT PROJ FROM USER_PROJ WHERE GID=?',
[job_wrapper.user_id])
162 row = c.fetchone()
163 c.close
164 native_spec += ' -P ' + row[0]
165 except:
166 log.debug(Cannot look up proj of user %s %
job_wrapper.user_id)
167 # /END ADD USER PROJ
also, in the config, define a default instead of using None:
self.user_proj_map_db = resolve_path( kwargs.get(
user_proj_map_db, database/user_proj_map.sqlite ), self.root )
one last note: there doesn't seem to be any error displayed to the user if
the job cannot be scheduled because the galaxy user doesn't have
permissions to use the user's project (although there is a log entry), but
the job will never be scheduled. so be sure the galaxy user has
permissions to submit to all possible projects.
___
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/
