problems compiling HDF5 in parallel

Accelerated Computing HPC Compilers Legacy PGI Compilers
1

Hello all,

I’m trying to compile HDF5 with MVAPICH build with PGI, but i’m running into a lot of problems and i don’t know how to resolve them. The .configure instruccion i’m using is

./configure --prefix=/home/c_ochoa/extras/paralelo/HDF5 --enable-parallel --with-zlib=/home/c_ochoa/extras/zlib --enable-fortran

and the CC=mpicc


the error is

pgcc 9.0-1 64-bit target on x86-64 Linux -tp penryn-64
Copyright 1989-2000, The Portland Group, Inc. All Rights Reserved.
Copyright 2000-2009, STMicroelectronics, Inc. All Rights Reserved.
./H5match_types
make all-am
make[3]: Entering directory /home/c_ochoa/extras/source/hdf5-1.8.3/fortran/src' .deps/H5match_types.Po:29: *** missing separator. Stop. make[3]: Leaving directory /home/c_ochoa/extras/source/hdf5-1.8.3/fortran/src’
make[2]: *** [all] Error 2
make[2]: Leaving directory `/home/c_ochoa/extras/source/hdf5-1.8.3/fortran/src’
make[1]: *** [all-recursive] Error 1

any help will be appreciated

thanks

2

Hi Carlos,

I tried to recreate the problem here, but HDF5 built fine for me. Though, I just ran configure and then make. Can you list the exact steps you did?

Also, can you post lines 26 to 31 of `/home/c_ochoa/extras/source/hdf5-1.8.3/fortran/src/.deps/H5match_types.Po’? Maybe this will help determining the cause of the problem.

  • Mat
3

Hi Mat,

Thanks for answering.

 The steps i followed are:
1 setting the next variables:
                setenv CC mpicc
                setenv CFLAGS "-O2 -Msignextend -V"
                setenv F77 mpif77
                setenv FC mpif90
                setenv F90 mpif90
                setenv FFLAGS "-L/usr/lib64 -O2 -w -V -fPIC"
                setenv CXX mpiCC
                setenv CXXFLAGS ""
                setenv CPP 'gcc -E'
                setenv CXXCPP 'gcc -E'
                setenv CPPFLAGS "-DNDEBUG -DpgiFortran"
2 Running 
./configure --prefix=/home/c_ochoa/extras/paralelo/HDF5 --enable-parallel  --with- zlib=/home/c_ochoa/extras/zlib --enable-fortran

3 Running 
            Make

When i run make is when i get the error… the lines for the file you ask me are the next:

I tried to compile again and the error is in other row, now here is where it appears (lines57-63)

57  ./H5Ppublic.h ./H5Eprivate.h ./H5Epublic.h ./H5Epubgen.h ./H5Lprivate.h
58
59  pgcc 9.0-1 64-bit target on x86-64 Linux -tp penryn-64
60  Copyright 1989-2000, The Portland Group, Inc.  All Rights Reserved.
61  Copyright 2000-2009, STMicroelectronics, Inc.  All Rights Reserved.
62  H5.c :

The error was marked at row 59.

thanks

4

Hi Carlos,

Try removing the “-V” (version flag) from your build flags. Looks to me that when the dependency files are created, it also capturing the compiler version information.

  • Mat
5

Thanks a lot mat, it worked fine, now i just need to compile netcdf in parallel too.
LOL.