[FLASH-USERS] The problem "Segmentation fault"

Mon Jun 20 01:49:02 EDT 2011

Dear Anshu,

Thank you for the advice. 

This email contains two errors. One is the “gmake” error when I type “ ./setup Sedov –auto +ug +noio”. The other is a “gmake warning” when I type “./setup Sedov -auto”.

1. When I type “./setup Sedov –auto +ug +noio”, there is a error comes out in the step of gmake. 

The following is the last part of the error:

/opt/software/mpich2-gnu/lib/libmpich.a(simple_pmi.o): In function `PMI_Init':

simple_pmi.c:(.text+0x15c0): warning: Using 'gethostbyname' in statically linked applications requires at runtime the shared libraries from the glibc version used for linking

/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../lib64/librt.a(aio_misc.o): In function `__aio_enqueue_request':

(.text+0x247): undefined reference to `pthread_getschedparam'

/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../lib64/librt.a(aio_misc.o): In function `__aio_enqueue_request':

(.text+0x384): undefined reference to `pthread_cond_signal'

/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../lib64/librt.a(aio_misc.o): In function `__aio_enqueue_request':

(.text+0x421): undefined reference to `pthread_attr_init'

/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../lib64/librt.a(aio_misc.o): In function `__aio_enqueue_request':

(.text+0x42e): undefined reference to `pthread_attr_setdetachstate'

/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../lib64/librt.a(aio_misc.o): In function `__aio_enqueue_request':

(.text+0x43b): undefined reference to `pthread_attr_setstacksize'

/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../lib64/librt.a(aio_misc.o): In function `__aio_enqueue_request':

(.text+0x494): undefined reference to `pthread_attr_destroy'

/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../lib64/librt.a(aio_misc.o): In function `handle_fildes_io':

(.text+0x660): undefined reference to `pthread_getschedparam'

/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../lib64/librt.a(aio_misc.o): In function `handle_fildes_io':

(.text+0x694): undefined reference to `pthread_setschedparam'

/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../lib64/librt.a(aio_misc.o): In function `handle_fildes_io':

(.text+0x820): undefined reference to `pthread_cond_signal'

/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../lib64/librt.a(aio_misc.o): In function `handle_fildes_io':

(.text+0x8fd): undefined reference to `pthread_attr_init'

/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../lib64/librt.a(aio_misc.o): In function `handle_fildes_io':

(.text+0x90a): undefined reference to `pthread_attr_setdetachstate'

/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../lib64/librt.a(aio_misc.o): In function `handle_fildes_io':

(.text+0x9dd): undefined reference to `pthread_cond_timedwait'

/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../lib64/librt.a(aio_notify.o): In function `__aio_notify_only':

(.text+0xb7): undefined reference to `pthread_attr_init'

/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../lib64/librt.a(aio_notify.o): In function `__aio_notify_only':

(.text+0xc4): undefined reference to `pthread_attr_setdetachstate'

collect2: ld returned 1 exit status

gmake: *** [flash3] Error 1

I don’t know what happens.

2. When following the user’s guide, I type “./setup Sedov -auto”. I see a “warning”, and I don’t know whether it is ok.

The following is the “warning”:

/opt/hdf-1.6.5/lib/libhdf5.a(H5FDstream.o): In function `H5FD_stream_open':

H5FDstream.c:(.text+0x1207): warning: Using 'gethostbyname' in statically linked applications requires at runtime the shared libraries from the glibc version used for linking

SUCCESS

Is it ok? I see “SUCCESS” in the last line. 

At last, I want to tell you some information about my computer. It just has one computer, two Intel Xeon CPU. The system is CentOS 5.5. The version of MPI is mpich2-1.2.1. The version of gcc and gfortran is 4.1.2.

Best wishes,

Zhang Chao

From: Anshu Dubey 
Sent: Monday, June 20, 2011 11:19 AM
To: Zhang Chao 
Cc: flash-users at flash.uchicago.edu 
Subject: Re: [FLASH-USERS] The problem "Segmentation fault"

Dear Zhang,

Would you please try the following and let me know what happens.

Modify your setup line to
./setup Sedov -auto +ug +noio

then build using gmake and try to run it.

Also, could you tell us what are the versions of MPI, gfortran and gcc you are running.
Please make sure that your MPI library was built with the same version of gcc that
you are using to build FLASH.

Anshu

2011/6/19 Zhang Chao <walli1986 at hotmail.com>

  Dear all, 

  Can anyone help me? I met the “Segmentation fault” when I type “./flash3”.

  [walli at localhost object]$ ./flash3
  Segmentation fault

  It is really a big problem for me. I want to find a solution in the internet, but until now, I still cannot solve the problem.

  Best wishes,

  Zhang Chao

-- 
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Anshu Dubey
Associate Director and CS/Applications Group Leader          5747 S. Ellis Avenue 3rd Flr.
Flash Center for Computational Science                                773 834 2999 (office)
Fellow, Computation Institute                                                  312 420 0033 (mobile)
University of Chicago and Argonne National Laboratory        773 834 3230 (fax)
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