Running madgraph on slurm cluster

Asked by celik on 2020-10-03

I am trying to get madgraph working on a slurm cluster. I can generate a test event interactively, but when it comes to running madgraph in cluster mode , it fails with the following error.

Any help appreciated.

NUMBER OF CORES 1
launch in debug mode
^[[?1034h************************************************************
* *
* W E L C O M E to *
* M A D G R A P H 5 _ a M C @ N L O *
* M A D E V E N T *
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* * * *
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* * * * * 5 * * * * *
* * * * * *
* * * *
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* VERSION 2.7.3 20xx-xx-xx *
* *
* The MadGraph5_aMC@NLO Development Team - Find us at *
* https://server06.fynu.ucl.ac.be/projects/madgraph *
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* Type 'help' for in-line help. *
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************************************************************
INFO: load configuration from /truba/home/acelik/ISR_Jets/MG5_aMC_v2_7_3/ttbar_deneme/Cards/me5_configuration.txt
INFO: load configuration from /truba/home/acelik/ISR_Jets/MG5_aMC_v2_7_3/input/mg5_configuration.txt
INFO: load configuration from /truba/home/acelik/ISR_Jets/MG5_aMC_v2_7_3/ttbar_deneme/Cards/me5_configuration.txt
Using default text editor "vi". Set another one in ./input/mg5_configuration.txt
No valid eps viewer found. Please set in ./input/mg5_configuration.txt
No valid web browser found. Please set in ./input/mg5_configuration.txt
No valid SysCalc path found
import command /truba/home/acelik/ISR_Jets/MG5_aMC_v2_7_3/ttbar_deneme/bin/calistir
launch
stty: standard input: Inappropriate ioctl for device
The following switches determine which programs are run:
/==============================================================================\
| 1. Choose the shower/hadronization program ^[[1m shower^[[0m = ^[[32mPythia6^[[0m |
| 2. Choose the detector simulation program ^[[1mdetector^[[0m = ^[[32mDelphes^[[0m |
| 3. Choose an analysis package (plot/convert) ^[[1manalysis^[[0m = ^[[32mExRoot^[[0m |
| 4. Decay onshell particles ^[[1m madspin^[[0m = ^[[31mOFF^[[0m |
| 5. Add weights to events for new hypp. ^[[1mreweight^[[0m = ^[[01mNot Avail.^[[0m |
\==============================================================================/
Either type the switch number (1 to 5) to change its setting,
Set any switch explicitly (e.g. type 'shower=Pythia8' at the prompt)
Type 'help' for the list of all valid option
Type '0', 'auto', 'done' or just press enter when you are done.
The following switches determine which programs are run:
/==============================================================================\
| 1. Choose the shower/hadronization program ^[[1m shower^[[0m = ^[[32mPythia6^[[0m |
| 2. Choose the detector simulation program ^[[1mdetector^[[0m = ^[[32mDelphes^[[0m |
| 3. Choose an analysis package (plot/convert) ^[[1manalysis^[[0m = ^[[32mExRoot^[[0m |
| 4. Decay onshell particles ^[[1m madspin^[[0m = ^[[31mOFF^[[0m |
| 5. Add weights to events for new hypp. ^[[1mreweight^[[0m = ^[[01mNot Avail.^[[0m |
\==============================================================================/
Either type the switch number (1 to 5) to change its setting,
Set any switch explicitly (e.g. type 'shower=Pythia8' at the prompt)
Type 'help' for the list of all valid option
Type '0', 'auto', 'done' or just press enter when you are done.
The following switches determine which programs are run:
/==============================================================================\
| 1. Choose the shower/hadronization program ^[[1m shower^[[0m = ^[[32mPythia6^[[0m |
| 2. Choose the detector simulation program ^[[1mdetector^[[0m = ^[[32mDelphes^[[0m |
| 3. Choose an analysis package (plot/convert) ^[[1manalysis^[[0m = ^[[32mExRoot^[[0m |
| 4. Decay onshell particles ^[[1m madspin^[[0m = ^[[31mOFF^[[0m |
| 5. Add weights to events for new hypp. ^[[1mreweight^[[0m = ^[[01mNot Avail.^[[0m |
\==============================================================================/
Either type the switch number (1 to 5) to change its setting,
Set any switch explicitly (e.g. type 'shower=Pythia8' at the prompt)
Type 'help' for the list of all valid option
Type '0', 'auto', 'done' or just press enter when you are done.
The following switches determine which programs are run:
/==============================================================================\
| 1. Choose the shower/hadronization program ^[[1m shower^[[0m = ^[[32mPythia6^[[0m |
| 2. Choose the detector simulation program ^[[1mdetector^[[0m = ^[[32mDelphes^[[0m |
| 3. Choose an analysis package (plot/convert) ^[[1manalysis^[[0m = ^[[32mExRoot^[[0m |
| 4. Decay onshell particles ^[[1m madspin^[[0m = ^[[31mOFF^[[0m |
| 5. Add weights to events for new hypp. ^[[1mreweight^[[0m = ^[[01mNot Avail.^[[0m |
\==============================================================================/
Either type the switch number (1 to 5) to change its setting,
Set any switch explicitly (e.g. type 'shower=Pythia8' at the prompt)
Type 'help' for the list of all valid option
Type '0', 'auto', 'done' or just press enter when you are done.
^[[1;34m"OFF" not valid option for "reweight"^[[0m
The following switches determine which programs are run:
/==============================================================================\
| 1. Choose the shower/hadronization program ^[[1m shower^[[0m = ^[[32mPythia6^[[0m |
| 2. Choose the detector simulation program ^[[1mdetector^[[0m = ^[[32mDelphes^[[0m |
| 3. Choose an analysis package (plot/convert) ^[[1manalysis^[[0m = ^[[32mExRoot^[[0m |
| 4. Decay onshell particles ^[[1m madspin^[[0m = ^[[31mOFF^[[0m |
| 5. Add weights to events for new hypp. ^[[1mreweight^[[0m = ^[[01mNot Avail.^[[0m |
\==============================================================================/
Either type the switch number (1 to 5) to change its setting,
Set any switch explicitly (e.g. type 'shower=Pythia8' at the prompt)
Type 'help' for the list of all valid option
Type '0', 'auto', 'done' or just press enter when you are done.
The following switches determine which programs are run:
/==============================================================================\
| 1. Choose the shower/hadronization program ^[[1m shower^[[0m = ^[[32mPythia6^[[0m |
| 2. Choose the detector simulation program ^[[1mdetector^[[0m = ^[[32mDelphes^[[0m |
| 3. Choose an analysis package (plot/convert) ^[[1manalysis^[[0m = ^[[32mExRoot^[[0m |
| 4. Decay onshell particles ^[[1m madspin^[[0m = ^[[31mOFF^[[0m |
| 5. Add weights to events for new hypp. ^[[1mreweight^[[0m = ^[[01mNot Avail.^[[0m |
\==============================================================================/
Either type the switch number (1 to 5) to change its setting,
Set any switch explicitly (e.g. type 'shower=Pythia8' at the prompt)
Type 'help' for the list of all valid option
Type '0', 'auto', 'done' or just press enter when you are done.
^[[1;34mfound line : set nevents=200^[[0m
^[[1;34mThis answer is not valid for current question. Keep it for next question and use here default: EOF^[[0m
set nevents=200
^[[1mINFO: modify parameter nevents of the run_card.dat to 200 ^[[0m
Do you want to edit a card (press enter to bypass editing)?
/------------------------------------------------------------\
| ^[[31m1^[[0m. param : ^[[32mparam_card.dat^[[0m |
| ^[[31m2^[[0m. run : ^[[32mrun_card.dat^[[0m |
| ^[[31m3^[[0m. pythia : ^[[32mpythia_card.dat^[[0m |
| ^[[31m4^[[0m. delphes : ^[[32mdelphes_card.dat^[[0m |
\------------------------------------------------------------/
 you can also
   - enter the path to a valid card or banner.
   - use the 'set' command to modify a parameter directly.
     The set option works only for param_card and run_card.
     Type 'help set' for more information on this command.
   - call an external program (ASperGE/MadWidth/...).
     Type 'help' for the list of available command
 [^[[4m0^[[0m, done, 1, param, 2, run, 3, pythia, 4, enter path, ... ]
^[[1mThe answer to the previous question is not set in your input file^[[0m
^[[1mUse 0 value^[[0m
INFO: Update the dependent parameter of the param_card.dat
Generating 200 events with run name run_02
survey run_02
INFO: compile directory
^[[1;34mNot able to open file /truba/home/acelik/ISR_Jets/MG5_aMC_v2_7_3/ttbar_deneme/crossx.html since no program configured.Please set one in ./input/mg5_configuration.txt^[[0m
INFO: Using LHAPDF v6.2.3 interface for PDFs
compile Source Directory
Using random number seed offset = 66
INFO: Running Survey
Working on SubProcesses
INFO: P1_gg_ttx
^[[1;31mError detected in sub-command launch
write debug file /truba/home/acelik/ISR_Jets/MG5_aMC_v2_7_3/ttbar_deneme/run_02_tag_1_debug.log
If you need help with this issue please contact us on https://answers.launchpad.net/mg5amcnlo
MadGraph5Error : A compilation Error occurs when trying to compile /truba/home/acelik/ISR_Jets/MG5_aMC_v2_7_3/ttbar_deneme/SubProcesses/P1_gg_ttx.
        The compilation fails with the following output message:
            gfortran -O -w -fbounds-check -fPIC -ffixed-line-length-132 -w -c symmetry.f -I../../Source/
            gfortran -O -w -fbounds-check -fPIC -ffixed-line-length-132 -w -c idenparts.f -I../../Source/
            gfortran -o gensym symmetry.o idenparts.o -L../../lib/ -lmodel -lgeneric -lpdf -O -I/truba/home/acelik/ISR_Jets/MG5_aMC_v2_7_3/HEPTools/lhapdf6/include -L/truba/home/acelik/ISR_Jets/MG5_aMC_v2_7_3/HEPTools/lhapdf6/lib -lLHAPDF -lLHAPDF -L/truba/sw/centos7.3/lib/acml/5.3.1/gfortran64/lib -L/truba/sw/centos6.4/lib/openmpi/1.8.8-gcc/lib
            ../../lib//libpdf.a(pdf_lhapdf62.o): In function `std::_Rb_tree<int, std::pair<int const, (anonymous namespace)::PDFSetHandler>, std::_Select1st<std::pair<int const, (anonymous namespace)::PDFSetHandler> >, std::less<int>, std::allocator<std::pair<int const, (anonymous namespace)::PDFSetHandler> > >::_M_get_insert_unique_pos(int const&)':
            pdf_lhapdf62.cc:(.text+0xa7): undefined reference to `std::_Rb_tree_decrement(std::_Rb_tree_node_base*)'
            ../../lib//libpdf.a(pdf_lhapdf62.o): In function `std::_Rb_tree<int, std::pair<int const, (anonymous namespace)::PDFSetHandler>, std::_Select1st<std::pair<int const, (anonymous namespace)::PDFSetHandler> >, std::less<int>, std::allocator<std::pair<int const, (anonymous namespace)::PDFSetHandler> > >::_M_get_insert_hint_unique_pos(std::_Rb_tree_const_iterator<std::pair<int const, (anonymous namespace)::PDFSetHandler> >, int const&)':
            pdf_lhapdf62.cc:(.text+0x128): undefined reference to `std::_Rb_tree_decrement(std::_Rb_tree_node_base*)'
            pdf_lhapdf62.cc:(.text+0x170): undefined reference to `std::_Rb_tree_increment(std::_Rb_tree_node_base*)'
            ../../lib//libpdf.a(pdf_lhapdf62.o): In function `(anonymous namespace)::fstr_to_ccstr(char const*, unsigned long, bool)':
            pdf_lhapdf62.cc:(.text+0x23b): undefined reference to `operator new[](unsigned long)'
            pdf_lhapdf62.cc:(.text+0x28c): undefined reference to `std::basic_string<char, std::char_traits<char>, std::allocator<char> >::basic_string(char const*, std::allocator<char> const&)'
            pdf_lhapdf62.cc:(.text+0x299): undefined reference to `operator delete[](void*)'
            ../../lib//libpdf.a(pdf_lhapdf62.o): In function `lhapdf_getpdfsetlist_':
            pdf_lhapdf62.cc:(.text+0x2dc): undefined reference to `std::string::_Rep::_S_empty_rep_storage'
            pdf_lhapdf62.cc:(.text+0x30d): undefined reference to `std::string::append(char const*, unsigned long)'
            pdf_lhapdf62.cc:(.text+0x318): undefined reference to `std::string::append(std::string const&)'
            pdf_lhapdf62.cc:(.text+0x342): undefined reference to `std::string::_Rep::_M_dispose(std::allocator<char> const&)'
            pdf_lhapdf62.cc:(.text+0x359): undefined reference to `std::string::_Rep::_M_dispose(std::allocator<char> const&)'
            ../../lib//libpdf.a(pdf_lhapdf62.o): In function `lhapdf_setdatapath_':
            pdf_lhapdf62.cc:(.text+0x39d): undefined reference to `std::string::_Rep::_S_empty_rep_storage'
            pdf_lhapdf62.cc:(.text+0x3d1): undefined reference to `std::string::_Rep::_M_destroy(std::allocator<char> const&)'
            pdf_lhapdf62.cc:(.text+0x3e8): undefined reference to `std::string::_Rep::_M_dispose(std::allocator<char> const&)'
            ../../lib//libpdf.a(pdf_lhapdf62.o): In function `evolvepdfpm_':
            pdf_lhapdf62.cc:(.text+0x446): undefined reference to `__cxa_allocate_exception'
            pdf_lhapdf62.cc:(.text+0x45b): undefined reference to `std::basic_string<char, std::char_traits<char>, std::allocator<char> >::basic_string(char const*, std::allocator<char> const&)'
            pdf_lhapdf62.cc:(.text+0x466): undefined reference to `std::runtime_error::runtime_error(std::string const&)'
            pdf_lhapdf62.cc:(.text+0x47f): undefined reference to `std::string::_Rep::_M_dispose(std::allocator<char> const&)'
            pdf_lhapdf62.cc:(.text+0x491): undefined reference to `__cxa_throw'
            pdf_lhapdf62.cc:(.text+0x4a6): undefined reference to `std::string::_Rep::_M_dispose(std::allocator<char> const&)'
            pdf_lhapdf62.cc:(.text+0x4b3): undefined reference to `__cxa_free_exception'
            ../../lib//libpdf.a(pdf_lhapdf62.o): In function `structp_':
            pdf_lhapdf62.cc:(.text+0x4f0): undefined reference to `__cxa_allocate_exception'
            pdf_lhapdf62.cc:(.text+0x505): undefined reference to `std::basic_string<char, std::char_traits<char>, std::allocator<char> >::basic_string(char const*, std::allocator<char> const&)'
            pdf_lhapdf62.cc:(.text+0x510): undefined reference to `std::runtime_error::runtime_error(std::string const&)'
            pdf_lhapdf62.cc:(.text+0x529): undefined reference to `std::string::_Rep::_M_dispose(std::allocator<char> const&)'
            pdf_lhapdf62.cc:(.text+0x53b): undefined reference to `__cxa_throw'
            pdf_lhapdf62.cc:(.text+0x550): undefined reference to `std::string::_Rep::_M_dispose(std::allocator<char> const&)'
            pdf_lhapdf62.cc:(.text+0x55d): undefined reference to `__cxa_free_exception'
            ../../lib//libpdf.a(pdf_lhapdf62.o): In function `lhapdf_getdatapath_':
            pdf_lhapdf62.cc:(.text+0x581): undefined reference to `std::string::_Rep::_S_empty_rep_storage'
            pdf_lhapdf62.cc:(.text+0x5ba): undefined reference to `std::string::append(char const*, unsigned long)'
            pdf_lhapdf62.cc:(.text+0x5c5): undefined reference to `std::string::append(std::string const&)'
pdf_lhapdf62.cc:(.text+0x5c5): undefined reference to `std::string::append(std::string const&)'
            pdf_lhapdf62.cc:(.text+0x5f9): undefined reference to `std::string::_Rep::_M_dispose(std::allocator<char> const&)'
            pdf_lhapdf62.cc:(.text+0x61f): undefined reference to `std::string::_Rep::_M_dispose(std::allocator<char> const&)'
            ../../lib//libpdf.a(pdf_lhapdf62.o): In function `getdatapath_':
            pdf_lhapdf62.cc:(.text+0x64e): undefined reference to `std::string::_Rep::_S_empty_rep_storage'
            pdf_lhapdf62.cc:(.text+0x687): undefined reference to `std::string::append(char const*, unsigned long)'
            pdf_lhapdf62.cc:(.text+0x692): undefined reference to `std::string::append(std::string const&)'
            pdf_lhapdf62.cc:(.text+0x6c6): undefined reference to `std::string::_Rep::_M_dispose(std::allocator<char> const&)'
            pdf_lhapdf62.cc:(.text+0x6ec): undefined reference to `std::string::_Rep::_M_dispose(std::allocator<char> const&)'
            ../../lib//libpdf.a(pdf_lhapdf62.o): In function `lhapdf_appenddatapath_':
            pdf_lhapdf62.cc:(.text+0x743): undefined reference to `std::basic_string<char, std::char_traits<char>, std::allocator<char> >::basic_string(std::string const&)'
            pdf_lhapdf62.cc:(.text+0x799): undefined reference to `std::__throw_bad_alloc()'
            pdf_lhapdf62.cc:(.text+0x7a6): undefined reference to `operator new(unsigned long)'
            pdf_lhapdf62.cc:(.text+0x7e6): undefined reference to `std::basic_string<char, std::char_traits<char>, std::allocator<char> >::basic_string(std::string const&)'
            pdf_lhapdf62.cc:(.text+0x811): undefined reference to `std::basic_string<char, std::char_traits<char>, std::allocator<char> >::basic_string(char const*, std::allocator<char> const&)'
            pdf_lhapdf62.cc:(.text+0x81b): undefined reference to `__cxa_begin_catch'
            pdf_lhapdf62.cc:(.text+0x832): undefined reference to `std::string::_Rep::_M_dispose(std::allocator<char> const&)'

Question information

Language:
English Edit question
Status:
Answered
For:
MadGraph5_aMC@NLO Edit question
Assignee:
No assignee Edit question
Last query:
2020-10-05
Last reply:
2020-10-05
celik (watzinki) said : #1

Anyone has any idea? Tried different version of gfortran but no success so far.

I guess that you have to contact you should check the documentation of your cluster to learn how to use the module available on the cluster.
Your issue is likely related to the fact that you have compile lhapdf with a version of gcc which is not available on the compute node (like the system gcc). Note that you have to re-compile lhapdf with a version of gcc which is available on the cluster.

Cheers,

Olivier

> On 5 Oct 2020, at 11:15, celik <email address hidden> wrote:
>
> Question #693244 on MadGraph5_aMC@NLO changed:
> https://answers.launchpad.net/mg5amcnlo/+question/693244
>
> celik posted a new comment:
> Anyone has any idea? Tried different version of gfortran but no success
> so far.
>
> --
> You received this question notification because you are an answer
> contact for MadGraph5_aMC@NLO.

celik (watzinki) said : #3

>>our issue is likely related to the fact that you have compile lhapdf with a version of gcc which is not available on the compute node (like the system gcc). Note that you have to re-compile lhapdf with a version of gcc which is available on the cluster.

Well ,I checked all the modules available on the cluster. Then downloaded lhapdf and compiled it with one of them , then included that module inside my shell script that is being used for job submission on cluster. However, I am getting the same error with job submission but interactively.

Hi,

When I see those lines in your above log:
 -L/truba/sw/centos7.3/lib/acml/5.3.1/gfortran64/lib -L/truba/sw/centos6.4/lib/openmpi/1.8.8-gcc/lib

This seems to be an "OS" inconsistency since one part is compiling for centos7 and the second is compile for centos6 ... In itself compilation for one OS should work with the next OS but this indicates that you have an issue with your module dependencies

Cheers,

Olivier

> On 5 Oct 2020, at 21:05, celik <email address hidden> wrote:
>
> Question #693244 on MadGraph5_aMC@NLO changed:
> https://answers.launchpad.net/mg5amcnlo/+question/693244
>
> Status: Answered => Open
>
> celik is still having a problem:
>>> our issue is likely related to the fact that you have compile lhapdf
> with a version of gcc which is not available on the compute node (like
> the system gcc). Note that you have to re-compile lhapdf with a version
> of gcc which is available on the cluster.
>
> Well ,I checked all the modules available on the cluster. Then
> downloaded lhapdf and compiled it with one of them , then included that
> module inside my shell script that is being used for job submission on
> cluster. However, I am getting the same error with job submission but
> interactively.
>
> --
> You received this question notification because you are an answer
> contact for MadGraph5_aMC@NLO.

Can you help with this problem?

Provide an answer of your own, or ask celik for more information if necessary.

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