failed in using raxmlHPC-MPI

[135128...@gmail.com]

Greetings raxml group!

I want to use raxml-mpi to construct phygenetic tree of one gene family, but I failed several time and got error informaiotn.  Bellow is my used script

-----------------------------------------------------

#!/bin/bash

#SBATCH --job-name=Raxml                        # the name of your job

#SBATCH --output=/scratch/bl697/LEA/PF10704/raxml-MPI.txt       # this is the file your output and errors go to

#SBATCH --time=01:00:00                         # 20 min, shorter time, quicker start, max run time

#SBATCH --workdir=/scratch/bl697/LEA/PF10704                    # your work directory

#SBATCH --mem=1000                              # 2GB of memory

#SBATCH -c10                                    # 10 cpus

# load necessary moudles

module purge

module load gcc/4.8.2

module load openmpi/1.6.5

module load raxml/8.2.12

# run my MPI executable

# Modify the cammand line as necessary

srun /packages/raxml/8.2.12/bin/raxmlHPC-MPI -N 1000 -m PROTGAMMAJTT  -p 20170808 -s /scratch/bl697/LEA/PF10704/allPF10704_pep.fas -n /scratch/bl697/LEA/PF10704/allPF10704_pep.tree -f a -x 2017080$

-------------------------------------------------------------

below is my error informaiton:

--------------------------------------------------------------------------------------------

raxmlHPC-MPI: axml.c:5521: analyzeRunId: Assertion `0' failed.

This is RAxML MPI Process Number: 0

Error character / not allowed in run ID

[cn35:173272] *** Process received signal ***

[cn35:173272] Signal: Aborted (6)

[cn35:173272] Signal code:  (-6)

[cn35:173272] [ 0] /lib64/libpthread.so.0(+0xf7e0)[0x7fc9b012a7e0]

[cn35:173272] [ 1] /lib64/libc.so.6(gsignal+0x35)[0x7fc9afdb94f5]

[cn35:173272] [ 2] /lib64/libc.so.6(abort+0x175)[0x7fc9afdbacd5]

[cn35:173272] [ 3] /lib64/libc.so.6(+0x2b66e)[0x7fc9afdb266e]

[cn35:173272] [ 4] /lib64/libc.so.6(__assert_perror_fail+0x0)[0x7fc9afdb2730]

[cn35:173272] [ 5] /packages/raxml/8.2.12/bin/raxmlHPC-MPI[0x40e105]

[cn35:173272] [ 6] /packages/raxml/8.2.12/bin/raxmlHPC-MPI[0x41a5ca]

[cn35:173272] [ 7] /lib64/libc.so.6(__libc_start_main+0x100)[0x7fc9afda5d20]

[cn35:173272] [ 8] /packages/raxml/8.2.12/bin/raxmlHPC-MPI[0x4060c5]

[cn35:173272] *** End of error message ***

srun: error: cn35: task 0: Aborted

----------------------------------------------------------------------------------------------

I discussed it with our adminstration group, they update the version of raxml, but there is not improvement.

Thanks for helps

Bobin

[Alexey Kozlov]

please change your run id (-n option), as suggested by the error message:

Error character / not allowed in run ID

If you want RAxML to create output files in a specific location, please
use -w option.

Best,
Alexey

> --
> You received this message because you are subscribed to the Google
> Groups "raxml" group.
> To unsubscribe from this group and stop receiving emails from it, send
> an email to raxml+un...@googlegroups.com
> <mailto:raxml+un...@googlegroups.com>.
> For more options, visit https://groups.google.com/d/optout.

[135128...@gmail.com]

Thank you very much, Alexey .

I have solved my problem following your suggestion.

Best1

Bobin

在 2019年2月2日星期六 UTC-7上午5:30:13，Alexey Kozlov写道：