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From [email protected] on March 20, 2014 01:25:40

abhinav@abhnav:~$ qhost -F mem_requested

HOSTNAME ARCH NCPU LOAD MEMTOT MEMUSE SWAPTO SWAPUS

global - - - - - - -
abhnav lx26-amd64 4 0.18 1.8G 913.0M 1.9G 301.5M
Host Resource(s): hc:mem_requested=1.801G
localhost

abhinav@abhnav:~$ segway --num-labels=4 train test.genomedata traindir4
traindir4/observations/chr21.0000.float32 (9411193, 9595548)
____ PROGRAM ENDED SUCCESSFULLY WITH STATUS 0 AT Thursday March 20 2014, 10:46:02 IST ____
queued 48: emt0.0.0.traindir4.ba32aef4afee11e3b8541803736f5e43 (mem_requested=2048M h_vmem=2048M h_stack=8M)

on interruption

^CTraceback (most recent call last):
File "/home/abhinav/arch/Linux-x86_64/bin/segway", line 9, in
load_entry_point('segway==1.1.0', 'console_scripts', 'segway')()
File "/home/abhinav/arch/Linux-x86_64/lib/python2.7/segway/run.py", line 3592, in main
return runner()
File "/home/abhinav/arch/Linux-x86_64/lib/python2.7/segway/run.py", line 3429, in call
self.run(_args, *_kwargs)
File "/home/abhinav/arch/Linux-x86_64/lib/python2.7/segway/run.py", line 3407, in run
self.run_train()
File "/home/abhinav/arch/Linux-x86_64/lib/python2.7/segway/run.py", line 3038, in run_train
instance_params = run_train_func(num_segs_range)
File "/home/abhinav/arch/Linux-x86_64/lib/python2.7/segway/run.py", line 3056, in run_train_singlethread
res = [self.run_train_instance()]
File "/home/abhinav/arch/Linux-x86_64/lib/python2.7/segway/run.py", line 2937, in run_train_instance
self.run_train_round(instance_index, round_index, **kwargs)
File "/home/abhinav/arch/Linux-x86_64/lib/python2.7/segway/run.py", line 2900, in run_train_round
restartable_jobs.wait()
File "/home/abhinav/arch/Linux-x86_64/lib/python2.7/segway/cluster/init.py", line 192, in wait
sleep(MIN_JOB_WAIT_SLEEP_TIME)
KeyboardInterrupt

qmon queue control->running tab (empty)
listed in pending jobs

Original issue: http://code.google.com/p/segway-genome/issues/detail?id=30

From jay.hesselberth on April 13, 2011 10:27:13

I'm trying to run a segmentation where I'd like to specify that all
label 0 segments be between 20 and 150, with a ruler of 1 bp. All
other segments have no constraints. The seg table I use is:

label len
0 20:150:1
1: 1::1

and I also use --ruler-scale=1.

However, when I run this, the label 0 segments all end up being
exactly 150 bases in size, with nothing between 20-150. This seems
very strange to me. I've attached a picture of one of the segments, the parameter files, run script and segment table.

Attachment: mmh.tar.gz pic.tiff

Original issue: http://code.google.com/p/segway-genome/issues/detail?id=14

From [email protected] on November 12, 2009 11:45:53

Current interface is clunky. Should be able to reuse same directories, find
everything that needs to be automatically regenerated, etc.

Original issue: http://code.google.com/p/segway-genome/issues/detail?id=6

From [email protected] on April 25, 2014 11:16:22

Hello,

We would like to use Segway on our cluster managed by OAR system ( http://oar.imag.fr/dokuwiki/doku.php ). Could you make necessary changes for this? If you require any information or help, I am willing to provide as much as I can.

Sincerely,

Sevgin

Original issue: http://code.google.com/p/segway-genome/issues/detail?id=31

From [email protected] on January 07, 2010 19:31:13

Make it UUID based from current directory instead.

Original issue: http://code.google.com/p/segway-genome/issues/detail?id=12

From jay.hesselberth on August 18, 2010 12:29:09

I migrated some segway training runs from one file system to another; this changed the root path and so the .inc files referenced by segway.inc and input.master changed. When I initiate an identify run, the gmtkTriangulate task raises and exception and exits the segway run cleanly:

/segway-projects/results/20100812/exp1/segway.str:1:70: error: /segway-results/results/20100812/exp1/auxiliary/segway.inc: No such file or directory
Parse Error in file '/segway-projects/results/20100812/exp1/segway.str': expecting variable type at or before line 7, near (TYPE_SEGCOUNTDOWN)
Exiting Program
Traceback (most recent call last):
File "/segway-build/arch/Linux-x86_64/bin/segway", line 8, in
load_entry_point('segway==0.2.0', 'console_scripts', 'segway')()
File "/segway-build/arch/Linux-x86_64/lib/python2.6/segway-0.2.0-py2.6.egg/segway/run.py", line 3694, in main
return runner()
File "/segway-build/arch/Linux-x86_64/lib/python2.6/segway-0.2.0-py2.6.egg/segway/run.py", line 3514, in call
self.run(_args, *_kwargs)
File "/segway-build/arch/Linux-x86_64/lib/python2.6/segway-0.2.0-py2.6.egg/segway/run.py", line 3487, in run
self.run_triangulate()
File "/segway-build/arch/Linux-x86_64/lib/python2.6/segway-0.2.0-py2.6.egg/segway/run.py", line 3084, in run_triangulate
self.run_triangulate_single(num_segs)
File "/segway-build/arch/Linux-x86_64/lib/python2.6/segway-0.2.0-py2.6.egg/segway/run.py", line 3077, in run_triangulate_single
prog(**kwargs)
File "build/bdist.linux-x86_64/egg/optbuild.py", line 78, in call
File "build/bdist.linux-x86_64/egg/optbuild.py", line 209, in run
File "build/bdist.linux-x86_64/egg/optbuild.py", line 191, in _getoutput
File "build/bdist.linux-x86_64/egg/optbuild.py", line 154, in _popen
File "build/bdist.linux-x86_64/egg/optbuild.py", line 54, in _returncode_error_factory
optbuild.ReturncodeError: /segway-build/arch/Linux-x86_64/bin/gmtkTriangulate returned 1

However, the gmtkViterbi task that uses input.master recognizes the error and raises and exception, but then (apparently) thinks it exited because it ran out of memory and launches another job with increased memory requirements (below; there are multiple of these errors in a row as it keeps trying to launch the same job repeatedly). Rather than doing this, it should exit cleanly as above because the model isn't correctly parsed.

root@ip-10-204-151-58
/segway-projects/results/20100818/exp1/20100818.identify.20100818/output/e/identify

cat vit999.20100818.identify.20100818.196ffc5aaadf11dfbaf712313b0a94cc
/segway-build/arch/Linux-x86_64/lib/python2.6/path-2.2-py2.6.egg/path.py:32:
DeprecationWarning: the md5 module is deprecated; use hashlib instead
/segway-build/arch/Linux-x86_64/lib/python2.6/optbuild-0.1.7-py2.6.egg/optbuild.py:294:
DeprecationWarning: object.new() takes no parameters
/segway-build/arch/Linux-x86_64/lib/python2.6/tables/leaf.py:415:
PerformanceWarning: The Leaf /supercontig_5/continuous is
exceeding the maximum recommended rowsize (32000000 bytes);
be ready to see PyTables asking for lots of memory and possibly slow
I/O. You may want to reduce the rowsize by trimming the value of
dimensions that are orthogonal (and preferably close) to the main
dimension of this leave. Alternatively, in case you have specified a
very small/large chunksize, you may want to increase/decrease it.
PerformanceWarning)
/segway-projects/results/20100812/exp1/params/input.master:1:70:
error: /segway-results/results/20100812/exp1/auxiliary/segway.inc: No
such file or directory
ERROR: In file '/segway-projects/results/20100812/exp1/params/input.master'
line 18, DT 'map_frameIndex_ruler', equation 'mod(p0, RULER_SCALE) ==
0 ': Invalid symbol at 'ruler_scale)==0'
Traceback (most recent call last):
File "/segway-build/arch/Linux-x86_64/bin/segway-task", line 8, in
load_entry_point('segway==0.2.0', 'console_scripts', 'segway-task')()
File "/segway-build/arch/Linux-x86_64/lib/python2.6/segway-0.2.0-py2.6.egg/segway/task.py",
line 242, in main
return task(_args)
File "/segway-build/arch/Linux-x86_64/lib/python2.6/segway-0.2.0-py2.6.egg/segway/task.py",
line 234, in task
TASKS[verb, kind](%28chrom, start, end%29, resolution, outfilename, *args)
File "/segway-build/arch/Linux-x86_64/lib/python2.6/segway-0.2.0-py2.6.egg/segway/task.py",
line 211, in run_viterbi_save_bed
output = VITERBI_PROG.getoutput(_args)
File "build/bdist.linux-x86_64/egg/optbuild.py", line 203, in getoutput
File "build/bdist.linux-x86_64/egg/optbuild.py", line 191, in _getoutput
File "build/bdist.linux-x86_64/egg/optbuild.py", line 154, in _popen
File "build/bdist.linux-x86_64/egg/optbuild.py", line 54, in
_returncode_error_factory
optbuild.ReturncodeError:
/segway-build/arch/Linux-x86_64/bin/gmtkViterbi returned 1

Original issue: http://code.google.com/p/segway-genome/issues/detail?id=13

From [email protected] on October 07, 2009 10:07:58

Suggested fix: change segway-task such that if an existing file is passed
as the argument, it will not rewrite another one.

Original issue: http://code.google.com/p/segway-genome/issues/detail?id=3

From [email protected] on April 27, 2012 13:40:34

What steps will reproduce the problem? 1. 2. 3. What is the expected output? What do you see instead? What version of the product are you using? On what operating system? Please provide any additional information below.

Original issue: http://code.google.com/p/segway-genome/issues/detail?id=23

From [email protected] on October 07, 2009 21:19:07

Closing remaining open files:
/homes/hoffman/projects/encode/genomedata.all4/chr3.genomedata... done
/homes/hoffman/projects/encode/genomedata.all4/chr12.genomedata... done
/homes/hoffman/projects/encode/genomedata.all4/chr13.genomedata... done
/homes/hoffman/projects/encode/genomedata.all4/chr20.genomedata... done
/homes/hoffman/projects/encode/genomedata.all4/chr5.genomedata... done
/homes/hoffman/projects/encode/genomedata.all4/chr15.genomedata... done
/homes/hoffman/projects/encode/genomedata.all4/chr9.genomedata... done
/homes/hoffman/projects/encode/genomedata.all4/chr16.genomedata... done
/homes/hoffman/projects/encode/genomedata.all4/chr22.genomedata... done
/homes/hoffman/projects/encode/genomedata.all4/chr17.genomedata... done
/homes/hoffman/projects/encode/genomedata.all4/chr2.genomedata... done
/homes/hoffman/projects/encode/genomedata.all4/chr10.genomedata... done
/homes/hoffman/projects/encode/genomedata.all4/chr1.genomedata... done
/homes/hoffman/projects/encode/genomedata.all4/chr7.genomedata... done
/homes/hoffman/projects/encode/genomedata.all4/chr4.genomedata... done
/homes/hoffman/projects/encode/genomedata.all4/chr19.genomedata... done
/homes/hoffman/projects/encode/genomedata.all4/chrX.genomedata... done
/homes/hoffman/projects/encode/genomedata.all4/chr11.genomedata... done
/homes/hoffman/projects/encode/genomedata.all4/chr14.genomedata... done
/homes/hoffman/projects/encode/genomedata.all4/chr8.genomedata... done
/homes/hoffman/projects/encode/genomedata.all4/chr6.genomedata... done
/homes/hoffman/projects/encode/genomedata.all4/chr18.genomedata... done
/homes/hoffman/projects/encode/genomedata.all4/chr21.genomedata... done
/homes/hoffman/projects/encode/genomedata.all4/chrY.genomedata... done

Original issue: http://code.google.com/p/segway-genome/issues/detail?id=5

From [email protected] on September 26, 2012 19:14:22

Error is described more here https://j.ee.washington.edu/trac/gmtk/ticket/343 .

The output/e//emt files will have an error similar to:
segway-1.2.0.dev_r9225-py2.7.egg/segway/data/segway-wrapper.sh: line 38: 3501 Segmentation fault (core dumped) "$@" > "$stdout_filename"

Original issue: http://code.google.com/p/segway-genome/issues/detail?id=26

From [email protected] on May 24, 2013 16:27:39

What steps will reproduce the problem? 1. Download gmtk from Noble lab website http://noble.gs.washington.edu/proj/segway/gmtk/gmtk-20091016.tar.gz 2. follow instructions in README.txt for compiling
in Makfile, set optflags to
OPTFLAGS=-g -O3 -march=nocona -mfpmath=sse -msse4
make clean
make depend
make linux
make depend
make What is the expected output? What do you see instead? Partial output from compiling gmtk

g++ -I. -I./../miscSupport -I./../IEEEFloatingpoint
-I./../featureFileIO -L. -L./../miscSupport
-L./../IEEEFloatingpoint -L./../featureFileIO -g -g -O3 -D_TABLE
-march=nocona -mfpmath=sse -msse2 -Wall -ansi -pedantic
-DOPTIMIZE_FOR_MEMORY_USAGE -DHASH_PRIME_SIZE -Wall -g -DMAIN -o
gmtkJT gmtkJT.o -lGMTK -lgmtkio -lmiscSupport -lIEEEsupport -lfl
-lm
/usr/bin/ld: cannot find -lgmtkio
/usr/bin/ld: cannot find -lfl
collect2: ld returned 1 exit status
make[1]: *** [gmtkJT] Error 1
make[1]: Leaving directory `/tmp/tmpljgMJz/gmtk-20091016/tksrc'
make: *** [all] Error 2
===== ERROR: Command failed: make "OPTFLAGS=$OPTFLAGS" =====
Cleaning up.
GMTK not installed.
What version of the product are you using? On what operating system? gtmk: gmtk-20091016
OS: Ububtu 12.04 LTS
gcc: 4.6.3 Please provide any additional information below. changing line 69 in featureFileIO/pfile.cc from
p = strstr(hdr, argname);

to:
p = (char *) strstr(hdr, argname);

will allow compilation

Original issue: http://code.google.com/p/segway-genome/issues/detail?id=28

From [email protected] on August 27, 2012 19:09:35

Traceback (most recent call last):
File "/net/noble/vol1/home/epaul9/arch/Linux/RHEL6/x86_64/bin/segway", line 8, in
load_entry_point('segway==1.2.0.dev- r9225 ', 'console_scripts', 'segway')()
File "/net/noble/vol1/home/epaul9/arch/Linux/RHEL6/x86_64/lib/python2.7/segway-1.2.0.dev_r9225-py2.7.egg/segway/run.py", line 2483, in main
return runner()
File "/net/noble/vol1/home/epaul9/arch/Linux/RHEL6/x86_64/lib/python2.7/segway-1.2.0.dev_r9225-py2.7.egg/segway/run.py", line 2312, in call
self.run(_args, *_kwargs)
File "/net/noble/vol1/home/epaul9/arch/Linux/RHEL6/x86_64/lib/python2.7/segway-1.2.0.dev_r9225-py2.7.egg/segway/run.py", line 2303, in run
self.run_identify_posterior()
File "/net/noble/vol1/home/epaul9/arch/Linux/RHEL6/x86_64/lib/python2.7/segway-1.2.0.dev_r9225-py2.7.egg/segway/run.py", line 2225, in run_identify_posterior
IdentifySaver(self)(world)
File "/net/noble/vol1/home/epaul9/arch/Linux/RHEL6/x86_64/lib/python2.7/segway-1.2.0.dev_r9225-py2.7.egg/segway/output.py", line 139, in call
bigbed_outfilename=self.make_filename(self.bigbed_filename, world))
File "/net/noble/vol1/home/epaul9/arch/Linux/RHEL6/x86_64/lib/python2.7/segway-1.2.0.dev_r9225-py2.7.egg/segway/layer.py", line 355, in layer
segmentation.save(outfilename, bigbed_outfilename)
File "/net/noble/vol1/home/epaul9/arch/Linux/RHEL6/x86_64/lib/python2.7/segway-1.2.0.dev_r9225-py2.7.egg/segway/layer.py", line 252, in save
ends = self.write(outfile)
File "/net/noble/vol1/home/epaul9/arch/Linux/RHEL6/x86_64/lib/python2.7/segway-1.2.0.dev_r9225-py2.7.egg/segway/layer.py", line 287, in write
self.write_trackline(outfile)
File "/net/noble/vol1/home/epaul9/arch/Linux/RHEL6/x86_64/lib/python2.7/segway-1.2.0.dev_r9225-py2.7.egg/segway/layer.py", line 278, in write_trackline
print >>final_outfile, " ".join(self.trackline)
TypeError

Original issue: http://code.google.com/p/segway-genome/issues/detail?id=25

From [email protected] on May 21, 2012 21:32:58

Hi segway support

I'm the applications manager of the Australian National Bioinformatics HPC facility (NCI-SFB). We have received a request from a user to provision segway on the facility, however we use PBS-pro. Would it be possible to implement PBS-pro support?

Thanks
Gerald

Dr Gerald Hartig
Bioinformatics Manager NCI-SFB
[email protected]

Original issue: http://code.google.com/p/segway-genome/issues/detail?id=24

From [email protected] on October 07, 2011 10:01:25

When I install gmtk-20091016, the following errors occur. How to deal with it? thanks.

ar: creating libGMTK.a
g++ -I. -I./../miscSupport -I./../IEEEFloatingpoint -I./../featureFileIO -L. -L./../miscSupport -L./../IEEEFloatingpoint -L./../featureFileIO -g -g -O3 -march=nocona -mfpmath=sse -msse3 -Wall -ansi -pedantic -DOPTIMIZE_FOR_MEMORY_USAGE -DHASH_PRIME_SIZE -Wall -g -DMAIN -o gmtkJT gmtkJT.o -lGMTK -lgmtkio -lmiscSupport -lIEEEsupport -lfl -lm
/usr/bin/ld: cannot find -lgmtkio
collect2: ld returned 1 exit status
make[1]: *** [gmtkJT] Error 1
make[1]: *** Waiting for unfinished jobs....
make[1]: Leaving directory `/home/wfz/Downloads/gmtk-20091016/tksrc'
make: *** [all] Error 2

Original issue: http://code.google.com/p/segway-genome/issues/detail?id=22

From [email protected] on August 11, 2011 08:37:06

Running segway-winner with python2.5.2 exits with warning " 'with' will become a reserved keyword in Python 2.6 "

Inserting "from future import with_statement" in winner.py, solves this problem.

Original issue: http://code.google.com/p/segway-genome/issues/detail?id=21

From [email protected] on May 11, 2011 16:59:18

What steps will reproduce the problem? 1. segway train --semi-supervised
2. segway identify What is the expected output? What do you see instead? Error from gmtkViterbi: ERROR: discrete observed random variable 'supervisionLabel', frame 0, line 78, specifies a feature element 6:6 that is out of discrete range ([3:5] inclusive) of observation matrix What version of the product are you using? On what operating system? segway 1.0 Please provide any additional information below. I am not sure but I think there might be some problem in train.tab for semi-supervised cases. The train.tab look like:
name value
distribution asinh_norm
dont_train_filename 3histones-semisuperivisedWU/auxiliary/dont_train.list
include_tracknames BroadHistoneK562H3k79me2StdAln_2Reps.norm5
include_tracknames AllLabsHistoneK562H3k36me3StdAln_4Reps.norm5
include_tracknames AllLabsHistoneK562H3k4me3StdAln_6Reps.norm5
include_tracknames supervisionLabel

So in inculde_tracknames have supervisionLabel. So when I run the identify on it get error from gmtkViterbi like:
ERROR: discrete observed random variable 'supervisionLabel', frame 0, line 78, specifies a feature element 6:6 that is out of discrete range ([3:5] inclusive) of observation matrix
Traceback (most recent call last):

It seems to be mismatch in train.tab tracknames and those for which it is trained.

I have also tried to remove supervisionLabel from the train.tab and run it still I am getting same Error. One more basic doubt when running semi-supervised identify do I have to give --semi-supervised=filename option or not.
I have run with both options.

Attachment: vit15.cpkc.WU.identify.tab.1eed73a27bad11e0b2960019b9e1892e train.tab

Original issue: http://code.google.com/p/segway-genome/issues/detail?id=18

From [email protected] on October 07, 2009 10:13:11

Fix. Allow specification of a number of BED files to segway-task that will
be laid down as extra int tracks.

Original issue: http://code.google.com/p/segway-genome/issues/detail?id=4

From [email protected] on November 13, 2009 18:03:27

Even for very large jobs, only 2G of maxvmem is reported.

This might be a problem with some upstream package (either DRMAA for LSF or
the Platform LSF API itself) using an unsigned int32 somewhere where size_t
should be used.

I haven't investigated much, but it is a problem found only at the Sanger
so far. At the EBI, I don't have this issue. At the EBI, the system
parameter setting LSF_UNIT_FOR_LIMITS is set to "MB" rather than the
default of "KB" (because the values reported are much smaller). But at
Sanger memhog is not installed so it's not as easy to investigate further.

Original issue: http://code.google.com/p/segway-genome/issues/detail?id=7

From [email protected] on November 14, 2009 13:35:26

This is part of the nativeSpecification for each clustering system.

Original issue: http://code.google.com/p/segway-genome/issues/detail?id=8

From [email protected] on November 24, 2009 14:36:11

Check the Viterbi output to ensure that labels are assigned for the whole
region. Do not repeat these jobs.

Original issue: http://code.google.com/p/segway-genome/issues/detail?id=10

From [email protected] on March 10, 2014 05:15:42

Following error is coming up while setting up segway
OGE : http://dl.dropbox.com/u/47200624/respin/ge2011.11.tar.gz working fine
GMTK,HDF5,NUMPY etc all installed successfully

Linux 3.8.0-19-generic #29-Ubuntu SMP x86_64 x86_64 x86_64 Ubuntu 13.04

python -m segway.cluster.sge_setup
Traceback (most recent call last):
File "/usr/lib/python2.7/runpy.py", line 151, in _run_module_as_main
mod_name, loader, code, fname = _get_module_details(mod_name)
File "/usr/lib/python2.7/runpy.py", line 101, in _get_module_details
loader = get_loader(mod_name)
File "/usr/lib/python2.7/pkgutil.py", line 464, in get_loader
return find_loader(fullname)
File "/usr/lib/python2.7/pkgutil.py", line 474, in find_loader
for importer in iter_importers(fullname):
File "/usr/lib/python2.7/pkgutil.py", line 430, in iter_importers
import(pkg)
File "/home/abhinav/arch/Linux-x86_64/lib/python2.7/segway/cluster/init.py", line 69, in
driver_name = get_driver_name(_session)
File "/home/abhinav/arch/Linux-x86_64/lib/python2.7/segway/cluster/init.py", line 65, in get_driver_name
raise ValueError(msg)
ValueError: unsupported distributed resource management system: OGS/GE 2011.11

Original issue: http://code.google.com/p/segway-genome/issues/detail?id=29

From [email protected] on October 05, 2009 17:14:48

This would be nice. For now you can simulate this in bash by using
something like --include-coords=<(cat file1.bed file2.bed <(zcat
file3.bed.gz)).

Original issue: http://code.google.com/p/segway-genome/issues/detail?id=2

From jay.hesselberth on May 12, 2011 15:54:53

In 1.1.0, segway-layer doesn't keep the track coloring from segway.bed.gz, they all end up being one color. Anybody else find this?

Original issue: http://code.google.com/p/segway-genome/issues/detail?id=19

From jay.hesselberth on April 22, 2011 17:04:03

In 1.0.2, if you invoke segway alone from the command line it throws a cryptic message, this is not how previous versions behaved; just need to check args length prior to this:

jayh@genomics-cluster ~/projects/gdtools/gdtools

segway
Traceback (most recent call last):
File "/common/arch/Darwin-i386/bin/segway", line 8, in
load_entry_point('segway==1.0.2', 'console_scripts', 'segway')()
File "/common/arch/Darwin-i386/lib/python2.7/site-packages/segway-1.0.2-py2.7.egg/segway/run.py", line 3509, in main
options, args = parse_options(args)
File "/common/arch/Darwin-i386/lib/python2.7/site-packages/segway-1.0.2-py2.7.egg/segway/run.py", line 3499, in parse_options
if args[0] == "train":
IndexError: list index out of range

Original issue: http://code.google.com/p/segway-genome/issues/detail?id=15

From jay.hesselberth on May 02, 2011 10:17:35

After test suite with segway-1.1.0.dev- r5739 : training runs fine, but identification (and possibly viterbi decoding) are broken; on the command line they go through the memory progression and exit (test results attached). In error logs, getting error like:

Traceback (most recent call last):
File "/common/arch/Darwin-i386/bin/segway-task", line 8, in
load_entry_point('segway==1.1.0.dev- r5739 ', 'console_scripts', 'segway-task')()
File "/common/arch/Darwin-i386/lib/python2.7/site-packages/setuptools-0.6c11-py2.7.egg/pkg_resources.py", line 318, in load_entry_point
File "/common/arch/Darwin-i386/lib/python2.7/site-packages/setuptools-0.6c11-py2.7.egg/pkg_resources.py", line 2221, in load_entry_point
File "/common/arch/Darwin-i386/lib/python2.7/site-packages/setuptools-0.6c11-py2.7.egg/pkg_resources.py", line 1954, in load
File "/common/arch/Darwin-i386/lib/python2.7/site-packages/segway-1.1.0.dev_r5739-py2.7.egg/segway/task.py", line 27, in
from run import (POSTERIOR_SCALE_FACTOR, read_posterior, POSTERIOR_PROG)
File "/common/arch/Darwin-i386/lib/python2.7/site-packages/segway-1.1.0.dev_r5739-py2.7.egg/segway/run.py", line 46, in
from .cluster import (make_native_spec, JobTemplateFactory, RestartableJob,
File "/common/arch/Darwin-i386/lib/python2.7/site-packages/segway-1.1.0.dev_r5739-py2.7.egg/segway/cluster/init.py", line 68, in
with Session() as _session:
File "build/bdist.macosx-10.4-x86_64/egg/drmaa/init.py", line 527, in enter
File "build/bdist.macosx-10.4-x86_64/egg/drmaa/init.py", line 274, in initialize
File "build/bdist.macosx-10.4-x86_64/egg/drmaa/wrappers.py", line 59, in init
File "build/bdist.macosx-10.4-x86_64/egg/drmaa/errors.py", line 90, in error_check
drmaa.errors.DrmCommunicationException: code 2: denied: host "node006.cluster.private" is neither submit nor admin host

Notably, there are no issues with backing down to segway 1.0.2 (e.g. this is not a problem with the drmaa library or SGE job queuing).

Attachment: test.tar.gz

Original issue: http://code.google.com/p/segway-genome/issues/detail?id=16

From [email protected] on May 17, 2011 09:33:43

What steps will reproduce the problem? 1. Using version 1.1.0 (issue not present with 1.0.2)
2. segway identify ...

All identification jobs are exiting on LSF system.
In all files identifydir/output/e/identify/vit..... it says
mcorerun exec: ``exec'' -- Permission denied

Original issue: http://code.google.com/p/segway-genome/issues/detail?id=20

From [email protected] on May 04, 2011 11:34:00

Using version 1.0.2 after training, segway identify genomedata traindir identifydir failed with error

IOError: [Errno 2] No such file or directory: path('identifydirname/params/input.master')

Copying the file from the traindir fixes the issue.

Original issue: http://code.google.com/p/segway-genome/issues/detail?id=17

From [email protected] on May 01, 2013 12:51:33

Hi,
Would it be possible to add the ability to use SLURM with Segway? SLURM has a DRMAA implementation. I am willing to help.

Sincerely,

Chuck Connolly

Original issue: http://code.google.com/p/segway-genome/issues/detail?id=27

From [email protected] on November 24, 2009 14:39:44

Switching to a new work unit/hive architecture might be better. Set the
ulimit using the script. Allow running multiple work units per script.

Original issue: http://code.google.com/p/segway-genome/issues/detail?id=11

From [email protected] on November 14, 2009 13:36:58

Allow a user to specify a Python function that will take information about
a job and set parameters. This would allow people to, say, switch queues
depending on job memory usage requirements.

Original issue: http://code.google.com/p/segway-genome/issues/detail?id=9

From [email protected] on September 30, 2009 18:11:00

What steps will reproduce the problem? 1. python install.py What is the expected output? What do you see instead? Expect success, get this instead:

"""
mh5@bc-14-1-01 ~/src/sci-util/segway
$ python install.py

Where should platform-specific files be installed?
[/nfs/users/nfs_m/mh5/arch/Linux-x86_64]

Where should new Python packages be installed?
[/nfs/users/nfs_m/mh5/arch/Linux-x86_64/lib/python2.5]

Found /nfs/users/nfs_m/mh5/arch/Linux-x86_64/lib/python2.5 already in your
PYTHONPATH!

Where should new scripts and executables be installed?
[/nfs/users/nfs_m/mh5/arch/Linux-x86_64/bin]

Found /nfs/users/nfs_m/mh5/arch/Linux-x86_64/bin already in your PATH!

Found your ~/.pydistutils.cfg! (hopefully the configuration matches)

Searching for HDF5...found!

Searching for Numpy...found!

Searching for segway...not found.
May I install segway and dependencies? (Y/n) [Y]

Searching for drmaa-python... not found.
May I download and install drmaa-python 1.0.3? (Y/n) [Y]
Where should LSF-DRMAA be installed? [/nfs/users/nfs_m/mh5/arch/Linux-x86_64]

if [ ! -e lsf_drmaa-1.0.3.tar.gz ]; then wget http://softlayer.dl.sourceforge.net/project/lsf-drmaa/lsf_drmaa/1.0.3/lsf_drmaa-1.0.3.tar.gz -O lsf_drmaa-1.0.3.tar.gz; fi
if [ ! -d lsf_drmaa-1.0.3 ]; then tar -xzf lsf_drmaa-1.0.3.tar.gz; fi
cd lsf_drmaa-1.0.3
./configure --prefix=/nfs/users/nfs_m/mh5/arch/Linux-x86_64
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking for style of include used by make... GNU
checking dependency style of gcc... gcc3
checking how to run the C preprocessor... gcc -E
checking for ranlib... ranlib
checking for a BSD-compatible install... /usr/bin/install -c
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking for a sed that does not truncate output... /bin/sed
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for fgrep... /bin/grep -F
checking for ld used by gcc... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
checking the name lister (/usr/bin/nm -B) interface... BSD nm
checking whether ln -s works... yes
checking the maximum length of command line arguments... 98304
checking whether the shell understands some XSI constructs... yes
checking whether the shell understands "+="... yes
checking for /usr/bin/ld option to reload object files... -r
checking how to recognize dependent libraries... pass_all
checking for ar... ar
checking for strip... strip
checking for ranlib... (cached) ranlib
checking command to parse /usr/bin/nm -B output from gcc object... ok
file: could not find any magic files!
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for dlfcn.h... yes
checking for objdir... .libs
checking if gcc supports -fno-rtti -fno-exceptions... no
checking for gcc option to produce PIC... -fPIC -DPIC
checking if gcc PIC flag -fPIC -DPIC works... yes
checking if gcc static flag -static works... yes
checking if gcc supports -c -o file.o... yes
checking if gcc supports -c -o file.o... (cached) yes
checking whether the gcc linker (/usr/bin/ld) supports shared libraries... yes
checking whether -lc should be explicitly linked in... no
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... yes
checking whether make sets $(MAKE)... (cached) yes
checking whether ln -s works... yes
checking for ragel... no
checking for rst2html... no
checking for rst2html.py... rst2html.py
checking for rst2latex... no
checking for rst2latex.py... rst2latex.py
checking whether gcc accepts -Wno-missing-field-initializers... no
checking whether gcc accepts -Wno-format-zero-length... yes
checking host system type... (cached) x86_64-unknown-linux-gnu
checking for the pthreads library -lpthreads... no
checking whether pthreads work without any flags... no
checking whether pthreads work with -Kthread... no
checking whether pthreads work with -kthread... no
checking for the pthreads library -llthread... no
checking whether pthreads work with -pthread... yes
checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE
checking if more special flags are required for pthreads... no
configure: checking for LSF
checking for LSF compile flags... -I/usr/local/lsf/7.0/include
checking for LSF library dir... /usr/local/lsf/7.0/linux2.6-glibc2.3-x86_64/lib
checking for main in -lnsl... yes
checking for main in -lm... yes
checking for usable LSF libraries/headers... *** The LSF test program
failed to link or run. See the file config.log
*** for the exact error that occured.
no
configure: error:
LSF libraries/headers not found;
add --with-lsf-inc and --with-lsf-lib with appropriate locations.
Error installing: LSF-DRMAA
Command failed: ./configure --prefix=/nfs/users/nfs_m/mh5/arch/Linux-x86_64

Would you like to try to continue the installation without this program?
(Y/n) [n]
"""

The problem is not actually that the LSF libraries and headers are not
found. If you look in config.log, you will find the problem is due to
undefined references to dlopen and friends. Linking on this system requires
the -ldl flag in LDFLAGS. This seems like an upstream bug for FedStage DRMAA. Please use labels and text to provide additional information. Need to submit bug report upstream. Until then, workaround is to run
LDFLAGS=-ldl python install.py

Original issue: http://code.google.com/p/segway-genome/issues/detail?id=1