On 12/08/2016, at 11:35 AM, Megan Aylward <aylwar...@gmail.com> wrote:* Edit to original issue.This only occurs when I try using the beast/lib/beast.jar file rather than the executable file in beast/bin. Is there any way to increase the JVM memory when running the file in bin rather than the .jar file?
On Thursday, August 11, 2016 at 2:45:34 PM UTC-6, Megan Aylward wrote:I am running into a similar error. Beast with SNAPP has been running ok, now I have increased the number of mcmc chains which requires me to increase the JVM memory. When I do this using 8 threads and running 24 steps it runs steps 0-6 then fails are step 7 with the error File error: ./step7/beast.xml.state (No such file or directory)Any idea why this could be?Thanks,Megan
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On 12/08/2016, at 8:45 AM, Megan Aylward <aylwar...@gmail.com> wrote:
I am running into a similar error. Beast with SNAPP has been running ok, now I have increased the number of mcmc chains which requires me to increase the JVM memory. When I do this using 8 threads and running 24 steps it runs steps 0-6 then fails are step 7 with the error File error: ./step7/beast.xml.state (No such file or directory)Any idea why this could be?Thanks,
Megan
On Sunday, December 6, 2015 at 1:58:56 PM UTC-7, Rebecca Harris wrote:
Hi all,
I am trying to run BFD tutorial before I run it with my own data. However, I’m having similar issues. I have BEAST 2.6.1, MODEL_SELECTION 1.5.2, and SNAPP 1.5.0 installed.
I’m having the error:
“File error: C\Users\abm\BEAST\2.6\SNAPP\examples\BFD_-tutorial\runA\step3\beast.xml.state (The system cannot find the file specified)
Any thoughts/news on this matter?
Amely
Loading package SNAPP v1.4.2
Probing: snap.addon.jar Loading package BEAST v2.5.2
Probing: beast.jar Probing: beast.src.jar Loading package MODEL_SELECTION v1.4.2
Probing: MODEL_SELECTION.addon.jar Loading package BEASTLabs v1.8.1
Probing: BEASTlabs.addon.jar Loading package BEAST v2.5.2
Probing: beast.jar Probing: beast.src.jar Starting step 0
Starting step 1
Starting step 2
Starting step 4
Starting step 3
Starting step 5
Starting step 6
Starting step 7
Finished step 3
Finished step 6
Finished step 7
Finished step 1
Finished step 0
Finished step 5
Finished step 2
Finished step 4
File error: /ddn/home5/r2175/ptmp/SNAPP/BFD_Dendro/A/runA/step7/beast.xml.state (No such file or directory)
I found a similar error a while back. It happened I was working on 24 cores, the full number available on the node I was using. When I dialed it back to 23 cores, the run worked.
Maybe a contention issue or something?
Mark
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for x in $(seq 0 23); do qsub -o run${x}.log jobfilename.sb ${x}; done