Open lassancejm opened 5 years ago
jasonsydes
commented
5 years ago Me too. I ended up altering the code here. I changed this:
super(TrimAndRecurseOnOutgroups, self).__init__(preemptable=True)to this:
memory = 7900000000
super(TrimAndRecurseOnOutgroups, self).__init__(memory=memory, preemptable=True)and that has done the trick for me so far. No warranty of course.
lassancejm
commented
5 years ago Thanks, I will give this a try
esrice
commented
5 years ago Me too. I ended up altering the code here. I changed this:
super(TrimAndRecurseOnOutgroups, self).__init__(preemptable=True)to this:
memory = 7900000000 super(TrimAndRecurseOnOutgroups, self).__init__(memory=memory, preemptable=True)and that has done the trick for me so far. No warranty of course.
Just wanted to confirm that I had the same problem and this fix worked. I had to give it about twice that much memory for a mammalian genome, though.
diekhans
commented
5 years ago Would you create a pull request with this change?
Edward S. Rice notifications@github.com writes:
Me too. I ended up altering the code here. I changed this:
super(TrimAndRecurseOnOutgroups, self).__init__(preemptable=True)to this:
memory = 7900000000 super(TrimAndRecurseOnOutgroups, self).__init__(memory=memory, preemptable=True)and that has done the trick for me so far. No warranty of course.
Just wanted to confirm that I had the same problem and this fix worked. I had to give it about twice that much memory for a mammalian genome, though.
-- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: https://github.com/ComparativeGenomicsToolkit/cactus/issues/76#issuecomment-531835161 Me too. I ended up altering the code here. I changed this:
super(TrimAndRecurseOnOutgroups, self).__init__(preemptable=True) to this: memory = 7900000000 super(TrimAndRecurseOnOutgroups, self).__init__(memory=memory, preemptable=True) and that has done the trick for me so far. No warranty of course.Just wanted to confirm that I had the same problem and this fix worked. I had to give it about twice that much memory for a mammalian genome, though.
— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or mute the thread.*
esrice
commented
5 years ago Sure, just did.
On Mon, Sep 16, 2019 at 5:50 PM Mark Diekhans notifications@github.com wrote:
Would you create a pull request with this change?
Edward S. Rice notifications@github.com writes:
Me too. I ended up altering the code here. I changed this:
super(TrimAndRecurseOnOutgroups, self).__init__(preemptable=True)to this:
memory = 7900000000 super(TrimAndRecurseOnOutgroups, self).__init__(memory=memory, preemptable=True)and that has done the trick for me so far. No warranty of course.
Just wanted to confirm that I had the same problem and this fix worked. I had to give it about twice that much memory for a mammalian genome, though.
-- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub:
https://github.com/ComparativeGenomicsToolkit/cactus/issues/76#issuecomment-531835161 Me too. I ended up altering the code here. I changed this:
super(TrimAndRecurseOnOutgroups, self).init(preemptable=True)
to this:
memory = 7900000000 super(TrimAndRecurseOnOutgroups, self).init(memory=memory, preemptable=True)
and that has done the trick for me so far. No warranty of course.
Just wanted to confirm that I had the same problem and this fix worked. I had to give it about twice that much memory for a mammalian genome, though.
— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or mute the thread.*
— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/ComparativeGenomicsToolkit/cactus/issues/76?email_source=notifications&email_token=ABLL5JOIFRQ5ZR4JKJ3U7VLQJ6TNDA5CNFSM4HHMKQTKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD6ZTMIY#issuecomment-531838499, or mute the thread https://github.com/notifications/unsubscribe-auth/ABLL5JNZIQCGKMZWF7O43ILQJ6TNDANCNFSM4HHMKQTA .
diekhans
commented
5 years ago Thanks!
The new default memory is too high for Travis. Can you come up with a default more similar to what was actually used before.
Mark
Edward S. Rice notifications@github.com writes:
Sure, just did.
On Mon, Sep 16, 2019 at 5:50 PM Mark Diekhans notifications@github.com wrote:
Would you create a pull request with this change?
Edward S. Rice notifications@github.com writes:
Me too. I ended up altering the code here. I changed this:
super(TrimAndRecurseOnOutgroups, self).__init__(preemptable=True)to this:
memory = 7900000000 super(TrimAndRecurseOnOutgroups, self).__init__(memory=memory, preemptable=True)and that has done the trick for me so far. No warranty of course.
Just wanted to confirm that I had the same problem and this fix worked. I had to give it about twice that much memory for a mammalian genome, though.
-- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub:
https://github.com/ComparativeGenomicsToolkit/cactus/issues/76#issuecomment-531835161 Me too. I ended up altering the code here. I changed this:
super(TrimAndRecurseOnOutgroups, self).init(preemptable=True)
to this:
memory = 7900000000 super(TrimAndRecurseOnOutgroups, self).init(memory=memory, preemptable=True)
and that has done the trick for me so far. No warranty of course.
Just wanted to confirm that I had the same problem and this fix worked. I had to give it about twice that much memory for a mammalian genome, though.
— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or mute the thread.*
— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/ComparativeGenomicsToolkit/cactus/issues/76?email_source=notifications&email_token=ABLL5JOIFRQ5ZR4JKJ3U7VLQJ6TNDA5CNFSM4HHMKQTKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD6ZTMIY#issuecomment-531838499, or mute the thread https://github.com/notifications/unsubscribe-auth/ABLL5JNZIQCGKMZWF7O43ILQJ6TNDANCNFSM4HHMKQTA .
-- You are receiving this because you commented. Reply to this email directly or view it on GitHub: https://github.com/ComparativeGenomicsToolkit/cactus/issues/76#issuecomment-531846650Sure, just did.
On Mon, Sep 16, 2019 at 5:50 PM Mark Diekhans notifications@github.com wrote:
Would you create a pull request with this change?
Edward S. Rice notifications@github.com writes:
Me too. I ended up altering the code here. I changed this:
super(TrimAndRecurseOnOutgroups, self).__init__(preemptable=True)to this:
memory = 7900000000 super(TrimAndRecurseOnOutgroups, self).__init__(memory=memory, preemptable=True)and that has done the trick for me so far. No warranty of course.
Just wanted to confirm that I had the same problem and this fix worked. I had to give it about twice that much memory for a mammalian genome, though.
-- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub:
https://github.com/ComparativeGenomicsToolkit/cactus/issues/76# issuecomment-531835161 Me too. I ended up altering the code here. I changed this:
super(TrimAndRecurseOnOutgroups, self).init(preemptable=True)
to this:
memory = 7900000000 super(TrimAndRecurseOnOutgroups, self).init(memory=memory, preemptable=True)
and that has done the trick for me so far. No warranty of course.
Just wanted to confirm that I had the same problem and this fix worked. I had to give it about twice that much memory for a mammalian genome, though.
— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or mute the thread.*
— You are receiving this because you commented. Reply to this email directly, view it on GitHub <https://github.com/ComparativeGenomicsToolkit/cactus/issues/76?email_source= notifications&email_token= ABLL5JOIFRQ5ZR4JKJ3U7VLQJ6TNDA5CNFSM4HHMKQTKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD6ZTMIY
issuecomment-531838499>,
or mute the thread https://github.com/notifications/unsubscribe-auth/ ABLL5JNZIQCGKMZWF7O43ILQJ6TNDANCNFSM4HHMKQTA .
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esrice
commented
5 years ago Sure, just added a new commit. I actually did need all that memory to run it, so of course allocating memory dynamically rather than hard-coding would be ideal, but I don't have enough experience will toil to figure out how to do this easily. I'll try to figure it out at some point.
jasonsydes
commented
5 years ago I spent half a day trying to figure this out (maybe 6 months ago; perhaps things have changed since then), but in the end retreated to editing the code. Perhaps the cactus/toil developers could direct us to the correct approach?
Hi,
I am seeing many jobs associated with the TrimAndRecurseOnOutgroups step failing due to lack of memory. I am using Slurm and toil v 3.19.