Error during Installation of DALTON 2013.2 on fedora

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ranga
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Error during Installation of DALTON 2013.2 on fedora

Post by ranga » 16 Apr 2014, 21:13

[ 4%] Building C object CMakeFiles/dalton.dir/DALTON/cc/crayio.c.o
/usr/local/DALTON-2013.2-Source/DALTON/cc/crayio.c: In function ‘PrintFileStats’:
/usr/local/DALTON-2013.2-Source/DALTON/cc/crayio.c:192:3: warning: implicit declaration of function ‘fflush’ [-Wimplicit-function-declaration]
/usr/local/DALTON-2013.2-Source/DALTON/cc/crayio.c:192:10: error: ‘stdout’ undeclared (first use in this function)
/usr/local/DALTON-2013.2-Source/DALTON/cc/crayio.c:192:10: note: each undeclared identifier is reported only once for each function it appears in
/usr/local/DALTON-2013.2-Source/DALTON/cc/crayio.c:193:3: warning: implicit declaration of function ‘fprintf’ [-Wimplicit-function-declaration]
/usr/local/DALTON-2013.2-Source/DALTON/cc/crayio.c:193:3: warning: incompatible implicit declaration of built-in function ‘fprintf’ [enabled by default]
/usr/local/DALTON-2013.2-Source/DALTON/cc/crayio.c:193:11: error: ‘stderr’ undeclared (first use in this function)
/usr/local/DALTON-2013.2-Source/DALTON/cc/crayio.c: In function ‘wopen_’:
/usr/local/DALTON-2013.2-Source/DALTON/cc/crayio.c:266:5: warning: incompatible implicit declaration of built-in function ‘fprintf’ [enabled by default]
/usr/local/DALTON-2013.2-Source/DALTON/cc/crayio.c:266:13: error: ‘stderr’ undeclared (first use in this function)
/usr/local/DALTON-2013.2-Source/DALTON/cc/crayio.c:285:5: warning: implicit declaration of function ‘sprintf’ [-Wimplicit-function-declaration]
/usr/local/DALTON-2013.2-Source/DALTON/cc/crayio.c:285:12: warning: incompatible implicit declaration of built-in function ‘sprintf’ [enabled by default]
/usr/local/DALTON-2013.2-Source/DALTON/cc/crayio.c: In function ‘getwa_’:
/usr/local/DALTON-2013.2-Source/DALTON/cc/crayio.c:329:12: error: ‘stdout’ undeclared (first use in this function)
/usr/local/DALTON-2013.2-Source/DALTON/cc/crayio.c:330:5: warning: incompatible implicit declaration of built-in function ‘fprintf’ [enabled by default]
/usr/local/DALTON-2013.2-Source/DALTON/cc/crayio.c:330:13: error: ‘stderr’ undeclared (first use in this function)
/usr/local/DALTON-2013.2-Source/DALTON/cc/crayio.c: In function ‘putwa_’:
/usr/local/DALTON-2013.2-Source/DALTON/cc/crayio.c:409:5: warning: implicit declaration of function ‘printf’ [-Wimplicit-function-declaration]
/usr/local/DALTON-2013.2-Source/DALTON/cc/crayio.c:409:5: warning: incompatible implicit declaration of built-in function ‘printf’ [enabled by default]
make[2]: *** [CMakeFiles/dalton.dir/DALTON/cc/crayio.c.o] Error 1
make[1]: *** [CMakeFiles/dalton.dir/all] Error 2
make: *** [all] Error 2

I am simply using basic commands, ./setup followed by cd build followed by make.

bast
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Re: Error during Installation of DALTON 2013.2 on fedora

Post by bast » 16 Apr 2014, 21:26

first please try this:

Code: Select all

man stdio.h
if you see nothing, you probably need this:

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sudo yum install glibc-headers

ranga
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Re: Error during Installation of DALTON 2013.2 on fedora

Post by ranga » 16 Apr 2014, 21:32

already tried, stdio.h is present

wildcat
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Re: Error during Installation of DALTON 2013.2 on fedora

Post by wildcat » 16 Apr 2014, 22:05

If stdio.h is present, but compiler complains about implicit declaration of fflush, fprintf, etc., then your compiler setup is broken.

First try to compile some simple C program like the following

Code: Select all

#include <stdio.h>

int main(int argc, const char* argv[])
{
    printf("Hello, World!\n");
    return 0;
}
If compilation fails, the compiler setup is broken, so the problem has nothing to do with DALTON.

P.S. From my personal experience I suggest that you try to avoid Fedora on a working machine. At least do not use the latest release if it is not few weeks old. Fedora is great for those who want to experience the bleeding edge, but might be buggy as hell right after a new release.

ranga
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Re: Error during Installation of DALTON 2013.2 on fedora

Post by ranga » 17 Apr 2014, 05:30

there is no problem with compiling the hello word c program. I am using ver 18 of Fedora (not the latest) and version of c (gcc) and c++(g++) (as listed by ./setup command is given below)
-- The C compiler identification is GNU 4.7.2
-- The CXX compiler identification is GNU 4.7.2

It is interesting that helloworld works with gcc but not with g++ or c++ compiler. Does crayio.c specifically require cxx compiler? or c compiler is fine? working on getting the c++ compiler fixed.

bast
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Re: Error during Installation of DALTON 2013.2 on fedora

Post by bast » 17 Apr 2014, 09:06

dear Ranga,
C compiler is fine. only external/xcfun requires a C++ compiler.
in other words all .c files only need a C compiler.
you should perhaps specify the compilers explicitly:
./setup --fc=gfortran --cc=gcc --cxx=g++
it is indeed strange that your g++ does not manage to compile the hello world.
good luck,
radovan

wildcat
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Re: Error during Installation of DALTON 2013.2 on fedora

Post by wildcat » 17 Apr 2014, 10:13

crayio.c should be compiled with gcc (C compiler), not with g++ (C++ compiler), because it is C source file, not C++.

In addition to

Code: Select all

-- The C compiler identification is GNU 4.7.2
-- The CXX compiler identification is GNU 4.7.2
CMake should also output the actual command for each and every compiler below.
Something like this

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-- Check for working C compiler: /usr/bin/gcc
-- Check for working C compiler: /usr/bin/gcc -- works
Could you confirm that C compiler is indeed gcc?

ranga
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Re: Error during Installation of DALTON 2013.2 on fedora

Post by ranga » 20 Apr 2014, 17:55

output of setup on the screen.

-- The Fortran compiler identification is GNU
-- The C compiler identification is GNU 4.7.2
-- The CXX compiler identification is GNU 4.7.2
-- Check for working Fortran compiler: /usr/bin/gfortran
-- Check for working Fortran compiler: /usr/bin/gfortran -- works
-- Detecting Fortran compiler ABI info
-- Detecting Fortran compiler ABI info - done
-- Checking whether /usr/bin/gfortran supports Fortran 90
-- Checking whether /usr/bin/gfortran supports Fortran 90 -- yes
-- Check for working C compiler: /usr/lib/ccache/gcc
-- Check for working C compiler: /usr/lib/ccache/gcc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working CXX compiler: /usr/lib/ccache/g++
-- Check for working CXX compiler: /usr/lib/ccache/g++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Performing Test COMPILER_UNDERSTANDS_FORTRAN03
-- Performing Test COMPILER_UNDERSTANDS_FORTRAN03 - Success
-- Math lib search order is MKL;ESSL;ATLAS;ACML;SYSTEM_NATIVE
-- You can select a specific type by defining for instance -D BLAS_TYPE=ATLAS or -D LAPACK_TYPE=ACML
-- or by redefining MATH_LIB_SEARCH_ORDER
-- Found BLAS: ATLAS (/lib/atlas/libf77blas.so;/lib/atlas/libcblas.so;/lib/atlas/libatlas.so)
-- Found LAPACK: ATLAS (/lib/atlas/libatlas.so;/lib/atlas/liblapack.so)
-- Configuring done
-- Generating done
-- Build files have been written to: /usr/local/DALTON-2013.2-Source/build

configure step is done
now you need to compile the sources:
$ cd build
$ make

It seems that gcc and g++ works.
I have already tried to reinstall gcc & g++ compiler but it did not help

janus
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Re: Error during Installation of DALTON 2013.2 on fedora

Post by janus » 21 Apr 2014, 12:04

Do you have /usr/bin/gcc and /usr/bin/g++? I see that you use /usr/bin/gfortran, so you could try and use these instead of /usr/lib/ccache/gcc and /usr/lib/ccache/g++. Something like:

./setup --fc=/usr/bin/gfortran --cc=/usr/bin/gcc --cxx=/usr/bin/g++ (...)

wildcat
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Re: Error during Installation of DALTON 2013.2 on fedora

Post by wildcat » 21 Apr 2014, 15:56

janus wrote:Do you have /usr/bin/gcc and /usr/bin/g++? I see that you use /usr/bin/gfortran, so you could try and use these instead of /usr/lib/ccache/gcc and /usr/lib/ccache/g++.
If I'm not mistaken, /usr/lib/ccache/gcc and /usr/lib/ccache/g++ are just symlinks to "ccache gcc" and "ccache g++" respectively, so this is unlikely to help.

I still think that compiler setup is broken: gcc does not complain about missing header stdio.h, but it complains about stdout being undeclared. So I suggest first to reinstall GCC compilers and related packages using something like

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sudo yum reinstall ccache gcc gcc-c++ gcc-gfortran glibc-headers

ranga
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Re: Error during Installation of DALTON 2013.2 on fedora

Post by ranga » 25 Apr 2014, 17:46

Finally, worked the idea from janus ./setup --fc=/usr/bin/gfortran --cc=/usr/bin/gcc --cxx=/usr/bin/g++ worked. reinstalling did not do anything as i told in my earlier post.

Thanks for all the help.

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