Testing/running in Cray operating system troubles.

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Testing/running in Cray operating system troubles.

Postby rsheppar » Fri Jan 06, 2017 5:44 pm

Hello All,
Sorry if I missed this being addressed already. I did look...
Abinit built fine in the Cray Compiling Environment (XE-6). It found the machine FFTW3 flavor anf the MPI libs, but took a pass on the libsci libraries for BLAS/LAPACK etc. I used a GNU environment and loaded Python 2.7.8. The problem comes with testing/running. The Cray does not use mpirun/mpiexec. A typical failure line would be as at the bottom of this note. So I decided to try running the water tutorial to see what that does. I receive the following:

./abinit < tbase1_x.files >&
-bash: syntax error near unexpected token `newline'

The tbase1_x.files file looks fine with no unprinted characters. Please let me knowwhat has to change.
Thanks in advance!
Ray
______________________________________________________________
No YAML Error found in [v7][t87][np=1]
Command /N/dc2/projects/ray/br2/abinit/abinit-8.0.8/src/98_main/abinit < /N/dc2/projects/ray/br2/abinit/abinit-8.0.8/tests/Test_suite/v7_t85-t86-t87-t88/t88 .stdin > /N/dc2/projects/ray/br2/abinit/abinit-8.0.8/tests/Test_suite/v7_t85-t86-t87-t88/t88.stdout 2> /N/dc2/projects/ray/br2/abinit/abinit-8.0.8/tests/Test_ suite/v7_t85-t86-t87-t88/t88.stderr
returned exit_code: 134

[v7][t88][np=1]: fldiff.pl fatal error:
Unable to open input file /N/dc2/projects/ray/br2/abinit/abinit-8.0.8/tests/Test_suite/v7_t85-t86-t87-t88/t88.out [file=t88.out]
[v7][t88][np=1]: fldiff.pl fatal error:
Unable to open input file /N/dc2/projects/ray/br2/abinit/abinit-8.0.8/tests/Test_suite/v7_t85-t86-t87-t88/t88o_DS1_EDOS [file=t88o_DS1_EDOS]
[v7][t88][np=1]: fldiff.pl fatal error:
Unable to open input file /N/dc2/projects/ray/br2/abinit/abinit-8.0.8/tests/Test_suite/v7_t85-t86-t87-t88/t88o_DS1_BXSF [file=t88o_DS1_BXSF]
[v7][t88][np=1]: fldiff.pl fatal error:
Unable to open input file /N/dc2/projects/ray/br2/abinit/abinit-8.0.8/tests/Test_suite/v7_t85-t86-t87-t88/t88o_DS1_NEST [file=t88o_DS1_NEST]
[v7][t88][np=1]: fldiff.pl fatal error:
Unable to open input file /N/dc2/projects/ray/br2/abinit/abinit-8.0.8/tests/Test_suite/v7_t85-t86-t87-t88/t88o_DS1_PHDOS [file=t88o_DS1_PHDOS]
[v7][t88][np=1]: fldiff.pl fatal error:
Unable to open input file /N/dc2/projects/ray/br2/abinit/abinit-8.0.8/tests/Test_suite/v7_t85-t86-t87-t88/t88o_DS2_PHDOS [file=t88o_DS2_PHDOS]
[v7][t88][np=1]: fldiff.pl fatal error:
Unable to open input file /N/dc2/projects/ray/br2/abinit/abinit-8.0.8/tests/Test_suite/v7_t85-t86-t87-t88/t88o_DS1_PHGAMMA [file=t88o_DS1_PHGAMMA]
[v7][t88][np=1]: fldiff.pl fatal error:
Unable to open input file /N/dc2/projects/ray/br2/abinit/abinit-8.0.8/tests/Test_suite/v7_t85-t86-t87-t88/t88o_DS2_PHGAMMA [file=t88o_DS2_PHGAMMA]
[v7][t88][np=1]: fldiff.pl fatal error:
Unable to open input file /N/dc2/projects/ray/br2/abinit/abinit-8.0.8/tests/Test_suite/v7_t85-t86-t87-t88/t88o_DS1_NOINTP_A2FW [file=t88o_DS1_NOINTP_A2FW]
[v7][t88][np=1]: fldiff.pl fatal error:
Unable to open input file /N/dc2/projects/ray/br2/abinit/abinit-8.0.8/tests/Test_suite/v7_t85-t86-t87-t88/t88o_DS1_A2FW [file=t88o_DS1_A2FW]
[v7][t88][np=1]Test was not expected to fail but subprocesses returned 134
libhugetlbfs [login1:6359]: WARNING: No mount point found for default huge page size. Using first available mount point.
libhugetlbfs [login1:6359]: WARNING: Hugepage size 2097152 unavailable[Thu Jan 5 04:14:16 2017] [unknown] Fatal error in MPI_Init: Other MPI error, error sta ck:
MPIR_Init_thread(525):
MPID_Init(225).......: channel initialization failed
MPID_Init(598).......: PMI2 init failed: 1

Program received signal SIGABRT: Process abort signal.

Backtrace for this error:
libhugetlbfs [login1:6359]: WARNING: New heap segment map at 0x10000000000 failed: Cannot allocate memory
#0 0x23A219CD in _gfortrani_backtrace at backtrace.c:258
#1 0x23A21040 in _gfortrani_backtrace_handler at compile_options.c:129
#2 0x210DA24F in __open_nocancel
#3 0x23C354BB in raise at pt-raise.c:42
#4 0x23CA4830 in abort at abort.c:92
#5 0x23AE1281 in MPID_Abort
#6 0x23ACA89F in MPIR_Handle_fatal_error
#7 0x23ACA991 in MPIR_Err_return_comm
#8 0x23AB2ADE in MPI_Init
#9 0x23A765E3 in mpi_init__
#10 0x20D89149 in __m_xmpi_MOD_xmpi_init at m_xmpi.F90:601
#11 0x20010DB7 in abinit at abinit.F90:215

No YAML Error found in [v7][t88][np=1]...
____________________________
rsheppar
 
Posts: 1
Joined: Thu Jan 05, 2017 7:30 am

Re: Testing/running in Cray operating system troubles.

Postby Jordan » Mon Jan 23, 2017 9:26 am

Hi,

The typical use is
[code]
./abinit < tbase1_x.files > log &
[/code/

Note that "<" means read the standard input from the following file while ">" means send the standard output to the following file.
Does this work ?
Cheers.
Jordan
Jordan
 
Posts: 281
Joined: Tue May 07, 2013 9:47 am


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