Beginner (#1) - [XIOS] Can not running nemo (#70) - Message List

[XIOS] Can not running nemo
 solved

I use NEMO release-4.0 and xios-2.5, and use gcc comlier and openMPI. I have compiled OCRA2_ICE_PISCES case of release-4.0, and used "mpirun -n 4 ./nemo" to run NEMO, but have an error. It shows that:

terminate called after throwing an instance of 'std::length_error'
what():  basic_string::_S_create
Program received signal SIGABRT: Process abort signal.
Backtrace for this error:
#0  0x7F017BBB46F7
#1  0x7F017BBB4D3E
#2  0x7F017AE942EF
#3  0x7F017AE94277
#4  0x7F017AE95967
#5  0x7F017CBE0AC4
#6  0x7F017CBDEA35
#7  0x7F017CBDEA62
#8  0x7F017CBDEC82
#9  0x7F017CC33A96
#10  0x7F017CC3DDC1
#11  0x7F017CC3F630
#12  0x7F017CC3F6EC
#13  0x1567038 in void xios::xml::CXMLParser::ParseInclude<xios::CGroupTemplate<xios::CField, xios::CFieldGroup, xios::CFieldAttributes> >(std::istream&, std::string const&, xios::CGroupTemplate<xios::CField, xios::CFieldGroup, xios::CFieldAttributes>&)
#14  0x13B46F7 in xios::CGroupTemplate<xios::CField, xios::CFieldGroup, xios::CFieldAttributes>::parse(xios::xml::CXMLNode&, bool)
#15  0x124A518 in xios::CContext::parse(xios::xml::CXMLNode&)
#16  0x15654E2 in void xios::xml::CXMLParser::ParseInclude<xios::CContext>(std::istream&, std::string const&, xios::CContext&)
#17  0x124A12F in xios::CContext::parse(xios::xml::CXMLNode&)
#18  0x1562A44 in xios::xml::CXMLParser::ParseStream(std::istream&, std::string const&, std::set<std::string, std::less<std::string>, std::allocator<std::string> > const&)
#19  0x15636B7 in xios::xml::CXMLParser::ParseFile(std::string const&, std::set<std::string, std::less<std::string>, std::allocator<std::string> > const&)
#20  0x1257C40 in xios::CXios::initClientSide(std::string const&, ompi_communicator_t*&, ompi_communicator_t*&)
#21  0x13CA99A in cxios_init_client
#22  0x109DFC2 in __idata_MOD_xios_initialize
#23  0x4160C3 in __nemogcm_MOD_nemo_init
#24  0x4195AC in __nemogcm_MOD_nemo_gcm
-------------------------------------------------------
Primary job  terminated normally, but 1 process returned
a non-zero exit code. Per user-direction, the job has been aborted.
-------------------------------------------------------
--------------------------------------------------------------------------
mpirun noticed that process rank 0 with PID 0 on node localhost exited on signal 6 (Aborted).

and when I run the GYRE of release-3.6 with xios-1.0, I also meet the same problem. So how to solve the problem? and I am a beginner.

  • Message #189

    Hi,

    What you describe: I use NEMO release-4.0 and xios-2.5, and use gcc comlier and openMPI. I have compiled OCRA2_ICE_PISCES case of release-4.0, and used "mpirun -n 4 ./nemo" looks fine. The error messages show very clearly that your problems are related to xios = the additional software used for outputs.

    So that you should check first that you've extracted and complied xios as indicated here: https://forge.ipsl.jussieu.fr/nemo/chrome/site/doc/NEMO/guide/html/install.html#extract-and-install-xios and also check that all the xml files needed for xios and located in the EXP* directory are indeed in the directory where you run the code.

    Then, aside from your output messages you've shown, is NEMO starting? Do you get an ocean.output file, or any other output file? Hope this helps

  • Message #206

    Mark as resolved without further updates.

Attachments

No attachments created.