Trying to use madgraph on PBS system, but fails with error messages

Hi Martin,

That page was outdated and was related to MG4 only. (I've added this information in that page)
In fact MG5 deals internally on how and when to submit a job on the cluster.
You just have to edit the file
input/mg5_configuration.txt
and have those lines inside:
# Default Running mode
# 0: single machine/ 1: cluster / 2: multicore
run_mode = 1

# Cluster Type [pbs|sge|condor|lsf|ge|slurm] Use for cluster run only
# And cluster queue

cluster_type = pbs
cluster_queue = None

Then you just have to run
/home/tmartin/madgraph/n1n1/bin/generate_events test -f

Cheers,

Olivier

On Sep 10, 2013, at 10:41 PM, TMartin <email address hidden> wrote:

> New question #235482 on MadGraph5:
> https://answers.launchpad.net/madgraph5/+question/235482
>
> I am using a PBS system to run madgraph, and I am getting the following error:
>
> #############################################
>
> load configuration from /home/tmartin/madgraph/n1n1/Cards/me5_configuration.txt
> load configuration from /home/tmartin/madgraph/input/mg5_configuration.txt
> load configuration from /home/tmartin/madgraph/n1n1/Cards/me5_configuration.txt
> Using default text editor "vi". Set another one in ./input/mg5_configuration.txt
> Using default eps viewer "evince". Set another one in ./input/mg5_configuration.txt
> Using default web browser "firefox". Set another one in ./input/mg5_configuration.txt
> generate_events test -f
> Will run in mode pythia
> Generating 50000 events with run name test
> survey test
> compile directory
> Error: /usr/lib64/firefox/firefox not found
> /usr/lib/firefox/firefox not found
> ^[[1;34mWARNING: information about "mass [23]" is missing using default value: 91.1876. ^[[0m^[[0m
> ^[[1;34mWARNING: information about "mass [15]" is missing using default value: 1.777. ^[[0m^[[0m
> ^[[1;34mWARNING: information about "mass [6]" is missing using default value: 175.0. ^[[0m^[[0m
> ^[[1;31mError detected in "generate_events test -f"
> write debug file /home/tmartin/madgraph/n1n1/test_tag_1_debug.log
> If you need help with this issue please contact us on https://answers.launchpad.net/madgraph5
> MadGraph5Error : A compilation Error occurs when trying to compile /home/tmartin/madgraph/n1n1/Source.
> The compilation fails with the following output message:
> gfortran -O -w -ffixed-line-length-132 -c -o gen_ximprove.o gen_ximprove.f
> gfortran -O -w -ffixed-line-length-132 -c -o ranmar.o ranmar.f
> gfortran -O -w -ffixed-line-length-132 -c -o rw_routines.o rw_routines.f
> gfortran: error trying to exec 'f951': execvp: No such file or directory
> make: *** [gen_ximprove.o] Error 1
> make: *** Waiting for unfinished jobs....
> gfortran: error trying to exec 'f951': execvp: No such file or directory
> make: *** [ranmar.o] Error 1
> gfortran: error trying to exec 'f951': execvp: No such file or directory
> make: *** [rw_routines.o] Error 1
>
> Please try to fix this compilations issue and retry.
> Help might be found at https://answers.launchpad.net/madgraph5.
> If you think that this is a bug, you can report this at https://bugs.launchpad.net/madgraph5^[[0m^[[0m
> quit
>
> #############################################
>
> I am using qsub to submit a batch script, which calls madgraph using the following line:
>
> /home/tmartin/madgraph/n1n1/bin/generate_events test -f
>
> I have gone through the instructions at https://cp3.irmp.ucl.ac.be/projects/madgraph/wiki/General-Scripts but it simply says that the default configuration should work out of the box for PBS.
>
> --
> You received this question notification because you are a member of
> MadTeam, which is an answer contact for MadGraph5.

Ah! That is simple to use.

Thank you.

A quick follow up question, if you don't mind...

I want to run a large series of rjobs. If I run madevent for Pythia/Delphes independent from using them automatically with generate_events, will it also shift the runs to the queue?

Thanks Olivier Mattelaer, that solved my question.

By the way, not sure if this is a big issue at all or not, but I thought I would mention that I get some strange messages when the code gets to the Pythia portion of the processing: (this is verbatim, copy/paste from the output)

Storing parton level results
End Parton
Running Pythia
WARNING:

          ********************************************************
                  STDHEP version 5.04.01 - Aug. 29, 2005
          ********************************************************

 STDXWOPEN WARNING: I/O is initialized for stdhep only

WARNING:

          ********************************************************
                  STDHEP version 5.04.01 - Aug. 29, 2005
          ********************************************************

 STDXWOPEN WARNING: I/O is initialized for stdhep only

WARNING:

          ********************************************************
                  STDHEP version 5.04.01 - Aug. 29, 2005
          ********************************************************

 STDXWOPEN WARNING: I/O is initialized for stdhep only

WARNING:

          ********************************************************
                  STDHEP version 5.04.01 - Aug. 29, 2005
          ********************************************************

 STDXWOPEN WARNING: I/O is initialized for stdhep only

WARNING:

          ********************************************************
                  STDHEP version 5.04.01 - Aug. 29, 2005
          ********************************************************

 STDXWOPEN WARNING: I/O is initialized for stdhep only

This sounds harmless.

Hi Olivier,

I have a similar problem while running Madgraph in cluster.

I tried your solution (of editing the mg5_configuration.txt file) but it doesn't help.

Error:
------------------------------------------

INFO: compile directory
Unhandled exception in thread started by <function call at 0x7f2e07754c80>
Traceback (most recent call last):
  File "/usr/lib64/python2.6/subprocess.py", line 478, in call
    p = Popen(*popenargs, **kwargs)
  File "/usr/lib64/python2.6/subprocess.py", line 642, in __init__
    errread, errwrite)
  File "/usr/lib64/python2.6/subprocess.py", line 1238, in _execute_child
    raise child_exception
OSError: [Errno 2] No such file or directory
compile Source Directory
Error detected in "generate_events test-f"
write debug file /lustre/user/swasti/Programs/MG5_aMC_v2_3_0/trial_tt/test-f_tag_1_debug.log
If you need help with this issue please contact us on https://answers.launchpad.net/madgraph5
MadGraph5Error : A compilation Error occurs when trying to compile /lustre/user/swasti/Programs/MG5_aMC_v2_3_0/trial_tt/Source.
        The compilation fails with the following output message:
            gcc -O -w -fbounds-check -fPIC -ffixed-line-length-132 -c -o combine_events.o combine_events.f
            gcc -O -w -fbounds-check -fPIC -ffixed-line-length-132 -o ../bin/internal/combine_events combine_events.o rw_events.o ranmar.o kin_functions.o open_file.o rw_routines.o alfas_functions.o setrun.o -L../lib/ -lmodel -lpdf
            /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64/crt1.o: In function `_start':
            (.text+0x20): undefined reference to `main'
            combine_events.o: In function `sorto3_':
            combine_events.f:(.text+0x7a): undefined reference to `_gfortran_runtime_error_at'
             combine_events.o:combine_events.f:(.text+0x12d): more undefined references to `_gfortran_runtime_error_at' follow
            combine_events.o: In function `writebanner_u_':
            combine_events.f:(.text+0x342): undefined reference to `_gfortran_st_write'
            combine_events.f:(.text+0x4b57): undefined reference to `_gfortran_runtime_error_at'
             rw_events.f:(.text+0x13b0): undefined reference to `_gfortran_transfer_character'
            ranmar.f:(.text+0x1202): undefined reference to `_gfortran_st_write_done'
            kin_functions.o: In function `phi_':
            kin_functions.f:(.text+0x111): undefined reference to `atan'
            kin_functions.f:(.text+0x12d): undefined reference to `atan'
            kin_functions.o: In function `four_momentum_set2_':
            rw_routines.f:(.text+0x29da): undefined reference to `_gfortran_string_index'
            rw_routines.f:(.text+0x351f): undefined reference to `_gfortran_st_close'
            alfas_functions.o: In function `mfrun_':
            alfas_functions.o: In function `newton1_':
            alfas_functions.f:(.text+0x247): undefined reference to `_gfortran_runtime_error_at'
            setrun.o: In function `get_pdfup_':
            setrun.f:(.text+0x37): undefined reference to `_gfortran_compare_string'
            setrun.f:(.text+0x86): undefined reference to `_gfortran_st_write'
            ../lib//libpdf.a(NNPDFDriver.o): In function `readpdfset_':
            NNPDFDriver.f:(.text+0x2013): undefined reference to `_gfortran_transfer_real'
            NNPDFDriver.f:(.text+0x2028): undefined reference to `_gfortran_st_read_done'
                 ../lib//libpdf.a(Ctq5Pdf.o): In function `polint_':
            Ctq5Pdf.f:(.text+0x38): undefined reference to `_gfortran_runtime_error_at'
            Ctq5Pdf.f:(.text+0x75): undefined reference to `_gfortran_runtime_error_at'
            Ctq5Pdf.f:(.text+0xc4): undefined reference to `_gfortran_runtime_error_at'
            Ctq5Pdf.f:(.text+0x108): undefined reference to `_gfortran_runtime_error_at'
            Ctq5Pdf.f:(.text+0x146): undefined reference to `_gfortran_runtime_error_at'
            ../lib//libpdf.a(Ctq5Pdf.o):Ctq5Pdf.f:(.text+0x174): more undefined references to `_gfortran_runtime_error_at' follow
            ../lib//libpdf.a(Ctq5Pdf.o): In function `polint_':
            Ctq5Pdf.f:(.text+0x2dd): undefined reference to `_gfortran_stop_numeric'
            Ctq5Pdf.f:(.text+0x33f): undefined reference to `_gfortran_runtime_error_at'
            Ctq5Pdf.f:(.text+0x365): undefined reference to `_gfortran_runtime_error_at'
       Ctq5Pdf.f:(.text+0x985): undefined reference to `_gfortran_st_read'
            Ctq5Pdf.f:(.text+0x1109): undefined reference to `_gfortran_runtime_error_at'
                 ../lib//libpdf.a(Partonx5.o): In function `partonx_':
            Partonx5.f:(.text+0x2a): undefined reference to `log'
            Partonx5.f:(.text+0x7d): undefined reference to `_gfortran_runtime_error_at'
            Partonx5.f:(.text+0xa0): undefined reference to `_gfortran_runtime_error_at'
            Partonx5.f:(.text+0x13c): undefined reference to `_gfortran_st_write'
            Partonx5.f:(.text+0x150): undefined reference to `_gfortran_transfer_character'
               ../lib//libpdf.a(Ctq6Pdf.o): In function `partonx6_':
            Ctq6Pdf.f:(.text+0x47d): undefined reference to `_gfortran_runtime_error_at'
            ../lib//libpdf.a(Ctq6Pdf.o):Ctq6Pdf.f:(.text+0x4a3): more undefined references to `_gfortran_runtime_error_at' follow
            ../lib//libpdf.a(Ctq6Pdf.o): In function `partonx6_':
            Ctq6Pdf.f:(.text+0x4c5): undefined reference to `pow'
               Ctq6Pdf.f:(.text+0x7e2): undefined reference to `_gfortran_runtime_error_at'
            Ctq6Pdf.f:(.text+0x817): undefined reference to `_gfortran_runtime_error_at'
            ../lib//libpdf.a(Ctq6Pdf.o):Ctq6Pdf.f:(.text+0x83a): more undefined references to `_gfortran_runtime_error_at' follow
            ../lib//libpdf.a(Ctq6Pdf.o): In function `partonx6_':
            Ctq6Pdf.f:(.text+0x14aa): undefined reference to `pow'
            ../lib//libpdf.a(Ctq6Pdf.o): In function `nextun6_':
            Ctq6Pdf.f:(.text+0x1c8d): undefined reference to `_gfortran_st_read'
            Ctq6Pdf.f:(.text+0x1cc6): undefined reference to `_gfortran_runtime_error_at'
            ../lib//libpdf.a(opendata.o): In function `opendata_':
            opendata.f:(.text+0x44): undefined reference to `_gfortran_runtime_error'
            opendata.f:(.text+0x1a7): undefined reference to `_gfortran_os_error'
            opendata.f:(.text+0x1c7): undefined reference to `_gfortran_concat_string'
            opendata.f:(.text+0x28e): undefined reference to `_gfortran_st_open'
            opendata.f:(.text+0x2c0): undefined reference to `_gfortran_runtime_error'
            ../lib//libpdf.a(opendata.o): In function `nextunopen_':
            opendata.f:(.text+0xcde): undefined reference to `_gfortran_st_inquire'
            opendata.f:(.text+0xd13): undefined reference to `_gfortran_stop_string'
            collect2: ld returned 1 exit status
            make: *** [../bin/internal/combine_events] Error 1

        Please try to fix this compilations issue and retry.
        Help might be found at https://answers.launchpad.net/madgraph5.
        If you think that this is a bug, you can report this at https://bugs.launchpad.net/madgraph5
---------------------------------------------------------

The python version in cluster is 2.6+ and also the updated gfortran /gcc are installed.
Also, LHAPDF and Fastjet installations worked smoothly.

It will be helpful if you can suggest something.

Regards,
Swasti

Hi,

This sounds like that part of the code is compile with gfortran and the rest with f77.
This typically happens if you use v4 model, where the compiler is typically hardcode in the model (to f77).
So changing the compiler of the model to f77 should fix your problem. Note that this should not be linked to the cluster
(The same should occur if you run locally)

Cheers,

Olivier

Hi Olivier,

Thank you very much for your reply.

Could you guide me a bit how that can be done, with respect to a particular model?
I tried setting the fortran compiler g77 in the mg5_configuration.txt file. Should that be sufficient, or changing the same file in the /v4Model/Cards/mg5_configuration.txt will help?

Cheers!
Swasti

Please open a new question to avoid to pollute this one with a different topic.

Cheers,

Olivier

Also, the same model works fine in my local machine with default settings. So the problem is only while running MG5 in cluster.