[netcdfgroup] Compile netcdf4 problem

• To: netcdfgroup@xxxxxxxxxxxxxxxx
• Subject: [netcdfgroup] Compile netcdf4 problem
• From: Wei Huang <huangwei@xxxxxxxx>
• Date: Tue, 3 May 2011 10:22:53 -0600

Hi, there,

I am trying to compile netcdf4 with parallel-enabled,
and got some compile errors. My configuration and compiler info and
the error messages are listed below.

Thanks for your help,

Wei Huang
huangwei@xxxxxxxx
VETS/CISL
National Center for Atmospheric Research
P.O. Box 3000 (1850 Table Mesa Dr.)
Boulder, CO 80307-3000 USA
(303) 497-8924

-----------------------------

1. Configure options:

 setenv MPICH_CC gcc

 setenv CC mpicc
 setenv FC mpif90

 configure \
        --prefix=/glade/home/huangwei/lib/netcdf/4.1.2 \
        --with-hdf5=/glade/home/huangwei/lib/hdf5/1.8.6 \
        --with-zlib=/fs/local/apps/zlib-1.2.3 \
        --with-szlib=/fs/local/apps/szip-2.0 \
        --enable-shared \
        --enable-parallel \
        --enable-ncgen4 \
        --enable-netcdf-4 \
        --enable-linux-lfs \
        --enable-parallel-tests


2. compiler info:

 icc -V

Intel(R) C Compiler for applications running on Intel(R) 64, Version 10.0    
Build 20070426 Package ID: l_cc_p_10.0.023
Copyright (C) 1985-2007 Intel Corporation.  All rights reserved.



 mpicc --version
gcc (GCC) 4.1.2 20080704 (Red Hat 4.1.2-50)
Copyright (C) 2006 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.



 mpif90 --version
ifort (IFORT) 10.1 20070913
Copyright (C) 1985-2007 Intel Corporation.  All rights reserved.



3. netcdf4 compile error message:

libtool: link: mpif90 -shared   .libs/fort-attio.o .libs/fort-control.o 
.libs/fort-dim.o .libs/fort-genatt.o .libs/fort-geninq.o .libs/fort-genvar.o 
.libs/fort-lib.o .libs/fort-misc.o .libs/fort-v2compat.o .libs/fort-vario.o 
.libs/fort-var1io.o .libs/fort-varaio.o .libs/fort-varmio.o .libs/fort-varsio.o 
.libs/fort-nc4.o   --whole-archive ../f90/.libs/libnetcdff90.a 
--no-whole-archive  -rpath /fs/local/64/apps/szip-2.0/lib -rpath 
/fs/local/share/src/libidn-1.19/lib -rpath /fs/local/64/apps/szip-2.0/lib 
-rpath /fs/local/share/src/libidn-1.19/lib -L/fs/local/apps/zlib-1.2.3/lib 
-L/glade/home/huangwei/lib/hdf5/1.8.6/lib -L/fs/local/apps/szip-2.0/lib 
-L/usr/kerberos/lib64 -lcurl -lgssapi_krb5 -lkrb5 -lk5crypto -lcom_err 
/fs/local/share/src/libidn-1.19/lib/libidn.so -L/fs/local/apps/netcdf-4.1.1/lib 
-lssl -lcrypto /glade/home/huangwei/lib/hdf5/1.8.6/lib/libhdf5_hl.a 
-L/fs/local/64/apps/szip-2.0/lib 
/glade/home/huangwei/lib/hdf5/1.8.6/lib/libhdf5.a 
/fs/local/64/apps/szip-2.0/lib/libsz.so -lz -L/fs/local/apps/mpich2-1.0.8p1/lib 
-L/fs/local/apps/intel/fce/10.1.008/lib 
-L/usr/lib/gcc/x86_64-redhat-linux/4.1.2/ 
-L/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../lib64 -lmpichf90 -lmpich 
-lpthread -lrt -lifport -lifcore -limf -lsvml -lm -lipgo -lintlc -lgcc_s 
-lirc_s -ldl -lc    -soname libnetcdff.so.5 -o .libs/libnetcdff.so.5.1.0
ifort: command line warning #10006: ignoring unknown option '-fwhole-archive'
ifort: command line warning #10006: ignoring unknown option '-fno-whole-archive'
ifort: command line warning #10156: ignoring option '-r'; no argument required
ifort: command line warning #10156: ignoring option '-r'; no argument required
ifort: command line warning #10156: ignoring option '-r'; no argument required
ifort: command line warning #10156: ignoring option '-r'; no argument required
ifort: command line warning #10156: ignoring option '-s'; no argument required
backend signals

fortcom: Severe: **Internal compiler error: internal abort** Please report this 
error along with the circumstances in which it occurred in a Software Problem 
Report.  Note: File and line given may not be explicit cause of this error.

ifort: error #10014: problem during multi-file optimization compilation (code 3)
make[3]: *** [libnetcdff.la] Error 3
make[3]: Leaving directory `/glade/home/huangwei/lib/netcdf-4.1.2/fortran'
make[2]: *** [all] Error 2
make[2]: Leaving directory `/glade/home/huangwei/lib/netcdf-4.1.2/fortran'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/glade/home/huangwei/lib/netcdf-4.1.2'
make: *** [all] Error 2

• References:
  • [netcdfgroup] netcdf-4.1.3-beta1 available
    • From: Ed Hartnett