Re: [raxml] Error message saying "RAxML wants to open for writing or appending can not be opened [mode: ab], exiting..."

[Alexandros Stamatakis]

I believe this must be a problem with either:

1. The scheduling system (could it be that you are starting 8 instances
of the PThreads code)

2. Your read/write permissions to the specific directory

I am afraid that the problem must be related somehow to the cluster
setup or usage, it's not a RAxML-related problem.

Also, please update to RAxML version 8.2.4

Alexis

On 30.10.2015 17:13, jw83...@gmail.com wrote:
> Hello,
>
> I am trying to run raxmlHPC-PTHREADS-SSE3 on scinet with command line
> saying :
>
> ….softwares/standard-RAxML-8.0.23/raxmlHPC-PTHREADS-SSE3 -f a -m
> PROTCATLG -T 8 -s fpps.bmge.phy -n fpps.bmge -x 123 -N 5
>
>
> and getting this error message:
>
> ----------------------------------------
> Begin PBS Prologue Thu Oct 29 13:35:41 EDT 2015 1446140141
> Job ID: 32118174.gpc-sched-ib0
> Username: jw833865
> Group: aroger
> Nodes: gpc-f137n009-ib0
> End PBS Prologue Thu Oct 29 13:35:42 EDT 2015 1446140142
> ----------------------------------------
> The file
> /bg01/homescinet/a/aroger/jw833865/BB2_Bordor1028_2/Bordor.10-28-2015.SGT/TEST/RAxML_info.fpps.bmge
> RAxML wants to open for writing or appending can not be opened [mode:
> ab], exiting ...
> ----------------------------------------
> Begin PBS Epilogue Thu Oct 29 13:35:48 EDT 2015 1446140148
> Job ID: 32118174.gpc-sched-ib0
> Username: jw833865
> Group: aroger
> Job Name: fpps.bmge-raxml
> Session: 4213
> Limits: neednodes=1:ppn=8,nodes=1:ppn=8,walltime=48:00:00
> Resources: cput=00:00:00,mem=0kb,vmem=0kb,walltime=00:00:02
> Queue: batch_ib
> Account:
> Nodes: gpc-f137n009-ib0
> Killing leftovers...
>
> End PBS Epilogue Thu Oct 29 13:35:49 EDT 2015 1446140149
> ----------------------------------------
>
> How can I fix this?
>
> Thank you for your time,
> Jiwob=n
>
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--
Alexandros (Alexis) Stamatakis

Research Group Leader, Heidelberg Institute for Theoretical Studies
Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology
Adjunct Professor, Dept. of Ecology and Evolutionary Biology, University
of Arizona at Tucson

www.exelixis-lab.org