archive:bioinformatic_tools:abyss
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archive:bioinformatic_tools:abyss [2010/05/11 04:32] jstjohn |
archive:bioinformatic_tools:abyss [2010/05/11 04:51] jstjohn |
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| </code> | </code> | ||
| + | FAIL ARRRG!! | ||
| + | |||
| + | Out of curiosity I decided to follow the example for how to run qsub on an MPI job over sun grid engine as documented on the campusrocks page. | ||
| + | To see the test and results look into the following directory on campusrocks: | ||
| + | /campus/BME235/test | ||
| + | |||
| + | I followed the example exactly and I get the following error (which is exactly the same as the one I get when trying to run ABySS!) | ||
| + | <code> | ||
| + | error: error: ending connection before all data received | ||
| + | error: | ||
| + | error reading job context from "qlogin_starter" | ||
| + | -------------------------------------------------------------------------- | ||
| + | A daemon (pid 9204) died unexpectedly with status 1 while attempting | ||
| + | to launch so we are aborting. | ||
| + | |||
| + | There may be more information reported by the environment (see above). | ||
| + | |||
| + | This may be because the daemon was unable to find all the needed shared | ||
| + | libraries on the remote node. You may set your LD_LIBRARY_PATH to have the | ||
| + | location of the shared libraries on the remote nodes and this will | ||
| + | automatically be forwarded to the remote nodes. | ||
| + | -------------------------------------------------------------------------- | ||
| + | -------------------------------------------------------------------------- | ||
| + | mpirun noticed that the job aborted, but has no info as to the process | ||
| + | that caused that situation. | ||
| + | -------------------------------------------------------------------------- | ||
| + | -------------------------------------------------------------------------- | ||
| + | mpirun was unable to cleanly terminate the daemons on the nodes shown | ||
| + | below. Additional manual cleanup may be required - please refer to | ||
| + | the "orte-clean" tool for assistance. | ||
| + | -------------------------------------------------------------------------- | ||
| + | campusrocks-0-7.local - daemon did not report back when launched | ||
| + | campusrocks-0-14.local - daemon did not report back when launched | ||
| + | </code> | ||
| + | |||
| + | I am now submitting an IT request to have someone look into this. | ||
| ===== References ===== | ===== References ===== | ||
| <refnotes>notes-separator: none</refnotes> | <refnotes>notes-separator: none</refnotes> | ||
| ~~REFNOTES cite~~ | ~~REFNOTES cite~~ | ||
archive/bioinformatic_tools/abyss.txt · Last modified: 2015/07/28 06:23 by ceisenhart
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