[Iplant-api-dev] LMOD errors

[Rion Dooley]

The script is failing because you are trying to do an iget command to transfer in data that should already be present in your work directory.  The use of iget in public apps on iPlant’s public systems  is not supported in Agave.  Aside from wasting quite a bit of compute time waiting for data to stage, it’s also a redundant operation. Agave will stage all your input files and folders to your job work directory prior to your job starting.

—
Rion

On May 28, 2015, at 3:54 PM, Duvick, Jonathan P [GDCBS] <jduvick at iastate.edu<mailto:jduvick at iastate.edu>> wrote:


This was still broken for me on 5/25, including the lmod error message in .err file.


My test jobs today (5/28) with ' gth-stampede-1.6.5u2 ' are also failing (or more accurately, jobs complete without error status, but have zero output)-- HOWEVER the .err file has a different set of messages, related to ipcservices path error (see below)

Error File:

 gdb006-example-9-remote-hpc-protein-spliced-alignments-ii-0001432844500123-5056a550b8-0001-007.err

Contents:

{
  "status" : "success",
  "message" : null,
  "version" : "2.1.0-r6d11c",
  "result" : { }
}ERROR: resolveRodsTarget: srcPath /iplant/home/ipcservices/GDB006gdna.fa does not exist
ERROR: getUtil: resolveRodsTarget status = -317000 USER_INPUT_PATH_ERR
ERROR: resolveRodsTarget: srcPath /iplant/home/ipcservices/GDB006prot.fa does not exist
ERROR: getUtil: resolveRodsTarget status = -317000 USER_INPUT_PATH_ERR
ERROR: resolveRodsTarget: srcPath /iplant/home/ipcservices/gth.lic does not exist
ERROR: getUtil: resolveRodsTarget status = -317000 USER_INPUT_PATH_ERR

Usage: bin/fastasplit.pl -i fastafile -s psize [-n npieces] [-o outputdir]


** This script splits the input FASTA file fastafile into multiple pieces
   fastafile1, fastafile2, ... .  How many piecess are generated depends on the
   arguments of either the -s option (each piece is at most psize MB) or the
   -n option (npieces files will be generated).

   The original fastafile remains untouched.

   If an output directory is specified with the -o option, then the pieces
   will be written to the speciefied directory.

Warning: Permanently added 'c408-802,129.114.67.60' (RSA) to the list of known hosts.
cat: cat: launcher.paramlistlauncher.paramlistcat: launcher.paramlistcat: launcher.paramlist: No such file or directory
: No such file or directory
: No such file or directory
: No such file or directory
cat: launcher.paramlistcat: launcher.paramlistcat: launcher.paramlist: No such file or directory
: No such file or directory
: No such file or directory
cat: launcher.paramlist: No such file or directory
cat: launcher.paramlist: No such file or directory
cat: launcher.paramlist: No such file or directory
cat: launcher.paramlist: No such file or directory
cat: launcher.paramlistcat: : No such file or directory
launcher.paramlistcat: : No such file or directory
cat: launcher.paramlistlauncher.paramlist: No such file or directory
: No such file or directorycat: launcher.paramlist
: No such file or directory
{
  "status" : "success",
  "message" : null,
  "version" : "2.1.0-r6d11c",
  "result" : { }
}

d


Jon Duvick
PlantGDB Manager
http://www.plantgdb.org/
Department of Genetics, Development and Cell Biology
2258 Molecular Biology Building
Iowa State University
Ames IA 50011

(515) 294-2360
(515) 294-6755 FAX
________________________________
From: iplant-api-dev-bounces at iplantcollaborative.org<mailto:iplant-api-dev-bounces at iplantcollaborative.org> <iplant-api-dev-bounces at iplantcollaborative.org<mailto:iplant-api-dev-bounces at iplantcollaborative.org>> on behalf of Barthelson, Roger A - (rogerab) <rogerab at email.arizona.edu<mailto:rogerab at email.arizona.edu>>
Sent: Thursday, May 28, 2015 1:38 PM
To: Duvick, Jonathan P [GDCBS]
Cc: Discussion of iPlant API development
Subject: [Iplant-api-dev] LMOD errors

Is this fixed yet or is it still difficult to identify the root cause?

Roger

--
Roger Barthelson Ph.D.
Scientific Analyst
iPlant Collaborative
BIO5 Institute, University of Arizona
Phone: 520-977-5249
Email: rogerab at email.arizona.edu<mailto:rogerab at email.arizona.edu>
Web: www.iplantcollaborative.org/<http://www.iplantcollaborative.org/>
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