# Problem with compiling HDF5 1.6 for parallel I/O **URL:** \ **Category:** Hdf-forum archives\ **Created:** [June 6, 2010, 12:19am UTC](https://forum.hdfgroup.org/t/problem-with-compiling-hdf5-1-6-for-parallel-i-o/1747 "2010-06-06T00:19:13Z")\ **Posts on this page:** 7\ **Page:** 1
**Author:** ![Kunal](https://forum.hdfgroup.org/letter_avatar_proxy/v4/letter/k/dec6dc/32.png) [@Kunal](https://forum.hdfgroup.org/u/Kunal)\ **Post date:** [June 6, 2010, 12:19am UTC](https://forum.hdfgroup.org/t/problem-with-compiling-hdf5-1-6-for-parallel-i-o/1747/1 "2010-06-06T00:19:13Z")
Hello: I am trying to compile and build hdf5 1.6 with parallel I/O on my laptop running Ubuntu 9.10 on a virtual machine. I have configured id with the following command: $CC=gcc F9X=/usr/bin/gfortran CPPFLAGS=-I/usr/include/mpi/ FFLAGS=-I/usr/include/mpich2/ ./configure --prefix=/home/kunalgrao/Desktop/hdf5\_parallel --enable-parallel --enable-fortran |tee configure\_parallel.log But when I do $ make I get the following error after some time : make[3]: Entering directory `/home/kunalgrao/Desktop/hdf5-1.6.10/fortran/testpar' /usr/bin/gfortran -I. -I/usr/include/mpich2/ -I. -I../src -c thyperslab\_wr.f90 -o thyperslab\_wr.o thyperslab\_wr.f90:54.26:      comm = MPI\_COMM\_WORLD                           1 Error: Symbol 'mpi\_comm\_world' at (1) has no IMPLICIT type thyperslab\_wr.f90:55.25:      info = MPI\_INFO\_NULL                          1 Error: Symbol 'mpi\_info\_null' at (1) has no IMPLICIT type make[3]: \*\*\* [thyperslab\_wr.lo] Error 1 make[3]: Leaving directory `/home/kunalgrao/Desktop/hdf5-1.6.10/fortran/testpar' Can you please tell me how to rectify this? I am attaching the log file for configure for your reference. Thanks & Regards, Kunal [configure\_parallel.log](https://hdf-discourse-1.s3.amazonaws.com/original/1X/f989af36bb6ffcb930c9163353fe88fb4498173d.log) (19.2 KB) ---
**Author:** ![Quincey\_Koziol](https://forum.hdfgroup.org/letter_avatar_proxy/v4/letter/q/dbc845/32.png) [@Quincey\_Koziol](https://forum.hdfgroup.org/u/Quincey_Koziol)\ **Post date:** [June 6, 2010, 3:02am UTC](https://forum.hdfgroup.org/t/problem-with-compiling-hdf5-1-6-for-parallel-i-o/1747/2 "2010-06-06T03:02:27Z")
Hi Kunal, > **···** > > On Jun 5, 2010, at 7:19 PM, kunal rao wrote: > > > Hello: > > > > I am trying to compile and build hdf5 1.6 with parallel I/O on my laptop running Ubuntu 9.10 on a virtual machine. > > > > I have configured id with the following command: > > > > $CC=gcc F9X=/usr/bin/gfortran CPPFLAGS=-I/usr/include/mpi/ FFLAGS=-I/usr/include/mpich2/ ./configure --prefix=/home/kunalgrao/Desktop/hdf5\_parallel --enable-parallel --enable-fortran |tee configure\_parallel.log > > > > But when I do $ make > > I get the following error after some time : > > > > make[3]: Entering directory `/home/kunalgrao/Desktop/hdf5-1.6.10/fortran/testpar' > > /usr/bin/gfortran -I. -I/usr/include/mpich2/ -I. -I../src -c thyperslab\_wr.f90 -o thyperslab\_wr.o > > thyperslab\_wr.f90:54.26: > > > >      comm = MPI\_COMM\_WORLD > >                           1 > > Error: Symbol 'mpi\_comm\_world' at (1) has no IMPLICIT type > > thyperslab\_wr.f90:55.25: > > > >      info = MPI\_INFO\_NULL > >                          1 > > Error: Symbol 'mpi\_info\_null' at (1) has no IMPLICIT type > > make[3]: \*\*\* [thyperslab\_wr.lo] Error 1 > > make[3]: Leaving directory `/home/kunalgrao/Desktop/hdf5-1.6.10/fortran/testpar' > > > > Can you please tell me how to rectify this? > > > > I am attaching the log file for configure for your reference. > >   First, you probably want the 1.8.5 release of HDF5, which should be released next week. Here's the link for a release candidate: > > ftp://ftp.hdfgroup.uiuc.edu/pub/outgoing/hdf5/hdf5-1.8.5-pre2/ > >   Then, you should use the 'mpicc' command from MPICH2 as your compiler, instead of trying to get the MPI include files and libraries correct. > >   Quincey ---
**Author:** ![robl](https://forum.hdfgroup.org/letter_avatar_proxy/v4/letter/r/e9a140/32.png) [@robl](https://forum.hdfgroup.org/u/robl)\ **Post date:** [June 7, 2010, 3:27pm UTC](https://forum.hdfgroup.org/t/problem-with-compiling-hdf5-1-6-for-parallel-i-o/1747/3 "2010-06-07T15:27:52Z")
Perhaps this is a transcription error, but I think you have your a typo or two in your environment variables: % CC=mpicc FC=mpif90 ./configure --enable-fortran ( the --enable-parallel is ok to keep but it is enabled when HDF5 sees you're building with an MPI compiler) ==rob > **···** > > On Sat, Jun 05, 2010 at 08:19:13PM -0400, kunal rao wrote: > > > Hello: > > > > I am trying to compile and build hdf5 1.6 with parallel I/O on my laptop > > running Ubuntu 9.10 on a virtual machine. > > > > I have configured id with the following command: > > > > $CC=gcc F9X=/usr/bin/gfortran CPPFLAGS=-I/usr/include/mpi/ > > FFLAGS=-I/usr/include/mpich2/ ./configure > > --prefix=/home/kunalgrao/Desktop/hdf5\_parallel --enable-parallel > > --enable-fortran |tee configure\_parallel.log > > -- > Rob Latham > Mathematics and Computer Science Division > Argonne National Lab, IL USA ---
**Author:** ![Kunal](https://forum.hdfgroup.org/letter_avatar_proxy/v4/letter/k/dec6dc/32.png) [@Kunal](https://forum.hdfgroup.org/u/Kunal)\ **Post date:** [June 6, 2010, 3:07am UTC](https://forum.hdfgroup.org/t/problem-with-compiling-hdf5-1-6-for-parallel-i-o/1747/4 "2010-06-06T03:07:33Z")
Hi Quincey, Thanks for your reply. I tried with mpicc as well..but still I got the same error.. Regards, Kunal > **···** > > On Sat, Jun 5, 2010 at 11:02 PM, Quincey Koziol \ wrote: > > > Hi Kunal, > > > > On Jun 5, 2010, at 7:19 PM, kunal rao wrote: > > > > Hello: > > > > I am trying to compile and build hdf5 1.6 with parallel I/O on my laptop > > running Ubuntu 9.10 on a virtual machine. > > > > I have configured id with the following command: > > > > $CC=gcc F9X=/usr/bin/gfortran CPPFLAGS=-I/usr/include/mpi/ > > FFLAGS=-I/usr/include/mpich2/ ./configure > > --prefix=/home/kunalgrao/Desktop/hdf5\_parallel --enable-parallel > > --enable-fortran |tee configure\_parallel.log > > > > But when I do $ make > > I get the following error after some time : > > > > make[3]: Entering directory > > `/home/kunalgrao/Desktop/hdf5-1.6.10/fortran/testpar' > > /usr/bin/gfortran -I. -I/usr/include/mpich2/ -I. -I../src -c > > thyperslab\_wr.f90 -o thyperslab\_wr.o > > thyperslab\_wr.f90:54.26: > > > >      comm = MPI\_COMM\_WORLD > >                           1 > > Error: Symbol 'mpi\_comm\_world' at (1) has no IMPLICIT type > > thyperslab\_wr.f90:55.25: > > > >      info = MPI\_INFO\_NULL > >                          1 > > Error: Symbol 'mpi\_info\_null' at (1) has no IMPLICIT type > > make[3]: \*\*\* [thyperslab\_wr.lo] Error 1 > > make[3]: Leaving directory > > `/home/kunalgrao/Desktop/hdf5-1.6.10/fortran/testpar' > > > > Can you please tell me how to rectify this? > > > > I am attaching the log file for configure for your reference. > > > > First, you probably want the 1.8.5 release of HDF5, which should be > > released next week. Here's the link for a release candidate: > > > > ftp://ftp.hdfgroup.uiuc.edu/pub/outgoing/hdf5/hdf5-1.8.5-pre2/ > > > > Then, you should use the 'mpicc' command from MPICH2 as your compiler, > > instead of trying to get the MPI include files and libraries correct. > > > > Quincey > > > > \_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_ > > Hdf-forum is for HDF software users discussion. > > Hdf-forum@hdfgroup.org > > [http://mail.hdfgroup.org/mailman/listinfo/hdf-forum\_hdfgroup.org](http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org) ---
**Author:** ![epourmal](https://forum.hdfgroup.org/letter_avatar_proxy/v4/letter/e/c67d28/32.png) [@epourmal](https://forum.hdfgroup.org/u/epourmal)\ **Post date:** [June 6, 2010, 3:58am UTC](https://forum.hdfgroup.org/t/problem-with-compiling-hdf5-1-6-for-parallel-i-o/1747/5 "2010-06-06T03:58:29Z")
Hi Kunal, Please make sure you have mpif.h under the include directories you specified. And it is better to use MPI fortran compiler (check if you have mpif90). Elena > **···** > > On Jun 5, 2010, at 10:07 PM, kunal rao wrote: > > > Hi Quincey, > > > > Thanks for your reply. I tried with mpicc as well..but still I got the same error.. > > > > Regards, > > Kunal > > > > On Sat, Jun 5, 2010 at 11:02 PM, Quincey Koziol \ wrote: > > Hi Kunal, > > > > On Jun 5, 2010, at 7:19 PM, kunal rao wrote: > > > > > Hello: > > > > > > I am trying to compile and build hdf5 1.6 with parallel I/O on my laptop running Ubuntu 9.10 on a virtual machine. > > > > > > I have configured id with the following command: > > > > > > $CC=gcc F9X=/usr/bin/gfortran CPPFLAGS=-I/usr/include/mpi/ FFLAGS=-I/usr/include/mpich2/ ./configure --prefix=/home/kunalgrao/Desktop/hdf5\_parallel --enable-parallel --enable-fortran |tee configure\_parallel.log > > > > > > But when I do $ make > > > I get the following error after some time : > > > > > > make[3]: Entering directory `/home/kunalgrao/Desktop/hdf5-1.6.10/fortran/testpar' > > > /usr/bin/gfortran -I. -I/usr/include/mpich2/ -I. -I../src -c thyperslab\_wr.f90 -o thyperslab\_wr.o > > > thyperslab\_wr.f90:54.26: > > > > > >      comm = MPI\_COMM\_WORLD > > >                           1 > > > Error: Symbol 'mpi\_comm\_world' at (1) has no IMPLICIT type > > > thyperslab\_wr.f90:55.25: > > > > > >      info = MPI\_INFO\_NULL > > >                          1 > > > Error: Symbol 'mpi\_info\_null' at (1) has no IMPLICIT type > > > make[3]: \*\*\* [thyperslab\_wr.lo] Error 1 > > > make[3]: Leaving directory `/home/kunalgrao/Desktop/hdf5-1.6.10/fortran/testpar' > > > > > > Can you please tell me how to rectify this? > > > > > > I am attaching the log file for configure for your reference. > > > >   First, you probably want the 1.8.5 release of HDF5, which should be released next week. Here's the link for a release candidate: > > > > ftp://ftp.hdfgroup.uiuc.edu/pub/outgoing/hdf5/hdf5-1.8.5-pre2/ > > > >   Then, you should use the 'mpicc' command from MPICH2 as your compiler, instead of trying to get the MPI include files and libraries correct. > > > >   Quincey > > > > \_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_ > > Hdf-forum is for HDF software users discussion. > > Hdf-forum@hdfgroup.org > > [http://mail.hdfgroup.org/mailman/listinfo/hdf-forum\_hdfgroup.org](http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org) > > > > \_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_ > > Hdf-forum is for HDF software users discussion. > > Hdf-forum@hdfgroup.org > > [http://mail.hdfgroup.org/mailman/listinfo/hdf-forum\_hdfgroup.org](http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org) ---
**Author:** ![Kunal](https://forum.hdfgroup.org/letter_avatar_proxy/v4/letter/k/dec6dc/32.png) [@Kunal](https://forum.hdfgroup.org/u/Kunal)\ **Post date:** [June 7, 2010, 4:35am UTC](https://forum.hdfgroup.org/t/problem-with-compiling-hdf5-1-6-for-parallel-i-o/1747/6 "2010-06-07T04:35:02Z")
Hi Elena, I tried with mpif90..but still get this error.. [configure\_parallel.log](https://hdf-discourse-1.s3.amazonaws.com/original/1X/8e2a229468ab14b063286f27682947b2fee08075.log) (19.3 KB) > **···** > > -------------------------------------------- > make[3]: Leaving directory > `/home/kunalgrao/Desktop/hdf5-1.6.10/fortran/test' > make[3]: Entering directory > `/home/kunalgrao/Desktop/hdf5-1.6.10/fortran/testpar' > mpif90 -I. -I. -I../src -c thyperslab\_wr.f90 -o thyperslab\_wr.o > thyperslab\_wr.f90:54.26: > >      comm = MPI\_COMM\_WORLD >                           1 > Error: Symbol 'mpi\_comm\_world' at (1) has no IMPLICIT type > thyperslab\_wr.f90:55.25: > >      info = MPI\_INFO\_NULL >                          1 > Error: Symbol 'mpi\_info\_null' at (1) has no IMPLICIT type > > ------------------------------------- > > Attaching my configuration output for your reference.. > > Thanks & Regards, > Kunal > > On Sat, Jun 5, 2010 at 11:58 PM, Elena Pourmal \wrote: > > > Hi Kunal, > > > > Please make sure you have mpif.h under the include directories you > > specified. And it is better to use MPI fortran compiler (check if you have > > mpif90). > > > > Elena > > > > On Jun 5, 2010, at 10:07 PM, kunal rao wrote: > > > > Hi Quincey, > > > > Thanks for your reply. I tried with mpicc as well..but still I got the same > > error.. > > > > Regards, > > Kunal > > > > On Sat, Jun 5, 2010 at 11:02 PM, Quincey Koziol \wrote: > > > > > Hi Kunal, > > > > > > On Jun 5, 2010, at 7:19 PM, kunal rao wrote: > > > > > > Hello: > > > > > > I am trying to compile and build hdf5 1.6 with parallel I/O on my laptop > > > running Ubuntu 9.10 on a virtual machine. > > > > > > I have configured id with the following command: > > > > > > $CC=gcc F9X=/usr/bin/gfortran CPPFLAGS=-I/usr/include/mpi/ > > > FFLAGS=-I/usr/include/mpich2/ ./configure > > > --prefix=/home/kunalgrao/Desktop/hdf5\_parallel --enable-parallel > > > --enable-fortran |tee configure\_parallel.log > > > > > > But when I do $ make > > > I get the following error after some time : > > > > > > make[3]: Entering directory > > > `/home/kunalgrao/Desktop/hdf5-1.6.10/fortran/testpar' > > > /usr/bin/gfortran -I. -I/usr/include/mpich2/ -I. -I../src -c > > > thyperslab\_wr.f90 -o thyperslab\_wr.o > > > thyperslab\_wr.f90:54.26: > > > > > >      comm = MPI\_COMM\_WORLD > > >                           1 > > > Error: Symbol 'mpi\_comm\_world' at (1) has no IMPLICIT type > > > thyperslab\_wr.f90:55.25: > > > > > >      info = MPI\_INFO\_NULL > > >                          1 > > > Error: Symbol 'mpi\_info\_null' at (1) has no IMPLICIT type > > > make[3]: \*\*\* [thyperslab\_wr.lo] Error 1 > > > make[3]: Leaving directory > > > `/home/kunalgrao/Desktop/hdf5-1.6.10/fortran/testpar' > > > > > > Can you please tell me how to rectify this? > > > > > > I am attaching the log file for configure for your reference. > > > > > > First, you probably want the 1.8.5 release of HDF5, which should be > > > released next week. Here's the link for a release candidate: > > > > > > ftp://ftp.hdfgroup.uiuc.edu/pub/outgoing/hdf5/hdf5-1.8.5-pre2/ > > > > > > Then, you should use the 'mpicc' command from MPICH2 as your compiler, > > > instead of trying to get the MPI include files and libraries correct. > > > > > > Quincey > > > > > > \_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_ > > > Hdf-forum is for HDF software users discussion. > > > Hdf-forum@hdfgroup.org > > > [http://mail.hdfgroup.org/mailman/listinfo/hdf-forum\_hdfgroup.org](http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org) > > > > \_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_ > > Hdf-forum is for HDF software users discussion. > > Hdf-forum@hdfgroup.org > > [http://mail.hdfgroup.org/mailman/listinfo/hdf-forum\_hdfgroup.org](http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org) > > > > \_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_ > > Hdf-forum is for HDF software users discussion. > > Hdf-forum@hdfgroup.org > > [http://mail.hdfgroup.org/mailman/listinfo/hdf-forum\_hdfgroup.org](http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org) ---
**Author:** ![Kunal](https://forum.hdfgroup.org/letter_avatar_proxy/v4/letter/k/dec6dc/32.png) [@Kunal](https://forum.hdfgroup.org/u/Kunal)\ **Post date:** [June 8, 2010, 12:03am UTC](https://forum.hdfgroup.org/t/problem-with-compiling-hdf5-1-6-for-parallel-i-o/1747/7 "2010-06-08T00:03:37Z")
Hi Quincey, Thanks for your reply. I used the latest release 1.8.5 and mpicc for compiling..and that worked fine.. Thanks a lot !! Regards, Kunal > **···** > > On Sat, Jun 5, 2010 at 11:02 PM, Quincey Koziol \ wrote: > > > Hi Kunal, > > > > On Jun 5, 2010, at 7:19 PM, kunal rao wrote: > > > > Hello: > > > > I am trying to compile and build hdf5 1.6 with parallel I/O on my laptop > > running Ubuntu 9.10 on a virtual machine. > > > > I have configured id with the following command: > > > > $CC=gcc F9X=/usr/bin/gfortran CPPFLAGS=-I/usr/include/mpi/ > > FFLAGS=-I/usr/include/mpich2/ ./configure > > --prefix=/home/kunalgrao/Desktop/hdf5\_parallel --enable-parallel > > --enable-fortran |tee configure\_parallel.log > > > > But when I do $ make > > I get the following error after some time : > > > > make[3]: Entering directory > > `/home/kunalgrao/Desktop/hdf5-1.6.10/fortran/testpar' > > /usr/bin/gfortran -I. -I/usr/include/mpich2/ -I. -I../src -c > > thyperslab\_wr.f90 -o thyperslab\_wr.o > > thyperslab\_wr.f90:54.26: > > > >      comm = MPI\_COMM\_WORLD > >                           1 > > Error: Symbol 'mpi\_comm\_world' at (1) has no IMPLICIT type > > thyperslab\_wr.f90:55.25: > > > >      info = MPI\_INFO\_NULL > >                          1 > > Error: Symbol 'mpi\_info\_null' at (1) has no IMPLICIT type > > make[3]: \*\*\* [thyperslab\_wr.lo] Error 1 > > make[3]: Leaving directory > > `/home/kunalgrao/Desktop/hdf5-1.6.10/fortran/testpar' > > > > Can you please tell me how to rectify this? > > > > I am attaching the log file for configure for your reference. > > > > First, you probably want the 1.8.5 release of HDF5, which should be > > released next week. Here's the link for a release candidate: > > > > ftp://ftp.hdfgroup.uiuc.edu/pub/outgoing/hdf5/hdf5-1.8.5-pre2/ > > > > Then, you should use the 'mpicc' command from MPICH2 as your compiler, > > instead of trying to get the MPI include files and libraries correct. > > > > Quincey > > > > \_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_ > > Hdf-forum is for HDF software users discussion. > > Hdf-forum@hdfgroup.org > > [http://mail.hdfgroup.org/mailman/listinfo/hdf-forum\_hdfgroup.org](http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org)