Re: Gadget2 on NCSA-Ember

From: Matthew Becker <beckermr_at_uchicago.edu>
Date: Mon, 24 Jan 2011 14:33:47 -0600

Try this out, but I cannot guarantee that this will fix the problem.

My *guess* is that you are linking in the wrong version of HDF5. The number
of arguments for the H5Acreate function changed between 1.6.x and 1.8.x (see
here http://www.hdfgroup.org/HDF5/doc/RM/RM_H5A.html#Annot-Create). You can
tell HDF5 1.8.x to be backwards compatible (see here
http://www.hdfgroup.org/HDF5/doc/RM/APICompatMacros.html). Try compiling
with this flag -DH5_USE_16_API . If that does not work, then the HDF5
library will have to be recompiled from source with 1.6.x support.

Matt

On Mon, Jan 24, 2011 at 2:11 PM, Agarwal, Shankar <sagarwal_at_ku.edu> wrote:

>
> Hi,
>
> I am trying to install Gadget2 on NCSA-Ember. I have edited the Makefile
> like this:
>
> CC = gcc -lmpi
> OPTIMIZE = -O3 -Wall
> GSL_INCL = -I/usr/apps/math/gsl/gnu/1.14/include
> GSL_LIBS = -L/usr/apps/math/gsl/gnu/1.14/lib
> FFTW_INCL= -I/usr/apps/math/fftw/gnu/3.2.2/include
> FFTW_LIBS = -L/usr/apps/math/fftw/gnu/3.2.2/lib
> MPICHLIB =
> HDF5INCL = -I/usr/apps/hdf/hdf5/v185-patch1/include
> HDF5LIB = -lhdf5 -lz -L/usr/apps/hdf/szip/lib -lsz
>
> The "make" command crashes at io.c. Please let me know if you can help me
> debug this.
>
> -Shankar
> KU Cosmology Group
>
>
> gcc -lmpi -O3 -Wall -DPERIODIC -DUNEQUALSOFTENINGS -DPEANOHILBERT
> -DWALLCLOCK -DPMGRID=128 -DSYNCHRONIZATION -DHAVE_HDF5
> -I/usr/apps/math/gsl/gnu/1.14/include
> -I/usr/apps/math/fftw/gnu/3.2.2/include
> -I/usr/apps/hdf/hdf5/v185-patch1/include -c -o main.o main.c
> gcc -lmpi -O3 -Wall -DPERIODIC -DUNEQUALSOFTENINGS -DPEANOHILBERT
> -DWALLCLOCK -DPMGRID=128 -DSYNCHRONIZATION -DHAVE_HDF5
> -I/usr/apps/math/gsl/gnu/1.14/include
> -I/usr/apps/math/fftw/gnu/3.2.2/include
> -I/usr/apps/hdf/hdf5/v185-patch1/include -c -o run.o run.c
> gcc -lmpi -O3 -Wall -DPERIODIC -DUNEQUALSOFTENINGS -DPEANOHILBERT
> -DWALLCLOCK -DPMGRID=128 -DSYNCHRONIZATION -DHAVE_HDF5
> -I/usr/apps/math/gsl/gnu/1.14/include
> -I/usr/apps/math/fftw/gnu/3.2.2/include
> -I/usr/apps/hdf/hdf5/v185-patch1/include -c -o predict.o predict.c
> gcc -lmpi -O3 -Wall -DPERIODIC -DUNEQUALSOFTENINGS -DPEANOHILBERT
> -DWALLCLOCK -DPMGRID=128 -DSYNCHRONIZATION -DHAVE_HDF5
> -I/usr/apps/math/gsl/gnu/1.14/include
> -I/usr/apps/math/fftw/gnu/3.2.2/include
> -I/usr/apps/hdf/hdf5/v185-patch1/include -c -o begrun.o begrun.c
> gcc -lmpi -O3 -Wall -DPERIODIC -DUNEQUALSOFTENINGS -DPEANOHILBERT
> -DWALLCLOCK -DPMGRID=128 -DSYNCHRONIZATION -DHAVE_HDF5
> -I/usr/apps/math/gsl/gnu/1.14/include
> -I/usr/apps/math/fftw/gnu/3.2.2/include
> -I/usr/apps/hdf/hdf5/v185-patch1/include -c -o endrun.o endrun.c
> gcc -lmpi -O3 -Wall -DPERIODIC -DUNEQUALSOFTENINGS -DPEANOHILBERT
> -DWALLCLOCK -DPMGRID=128 -DSYNCHRONIZATION -DHAVE_HDF5
> -I/usr/apps/math/gsl/gnu/1.14/include
> -I/usr/apps/math/fftw/gnu/3.2.2/include
> -I/usr/apps/hdf/hdf5/v185-patch1/include -c -o global.o global.c
> gcc -lmpi -O3 -Wall -DPERIODIC -DUNEQUALSOFTENINGS -DPEANOHILBERT
> -DWALLCLOCK -DPMGRID=128 -DSYNCHRONIZATION -DHAVE_HDF5
> -I/usr/apps/math/gsl/gnu/1.14/include
> -I/usr/apps/math/fftw/gnu/3.2.2/include
> -I/usr/apps/hdf/hdf5/v185-patch1/include -c -o timestep.o timestep.c
> gcc -lmpi -O3 -Wall -DPERIODIC -DUNEQUALSOFTENINGS -DPEANOHILBERT
> -DWALLCLOCK -DPMGRID=128 -DSYNCHRONIZATION -DHAVE_HDF5
> -I/usr/apps/math/gsl/gnu/1.14/include
> -I/usr/apps/math/fftw/gnu/3.2.2/include
> -I/usr/apps/hdf/hdf5/v185-patch1/include -c -o init.o init.c
> gcc -lmpi -O3 -Wall -DPERIODIC -DUNEQUALSOFTENINGS -DPEANOHILBERT
> -DWALLCLOCK -DPMGRID=128 -DSYNCHRONIZATION -DHAVE_HDF5
> -I/usr/apps/math/gsl/gnu/1.14/include
> -I/usr/apps/math/fftw/gnu/3.2.2/include
> -I/usr/apps/hdf/hdf5/v185-patch1/include -c -o restart.o restart.c
> gcc -lmpi -O3 -Wall -DPERIODIC -DUNEQUALSOFTENINGS -DPEANOHILBERT
> -DWALLCLOCK -DPMGRID=128 -DSYNCHRONIZATION -DHAVE_HDF5
> -I/usr/apps/math/gsl/gnu/1.14/include
> -I/usr/apps/math/fftw/gnu/3.2.2/include
> -I/usr/apps/hdf/hdf5/v185-patch1/include -c -o io.o io.c
> io.c: In function ‘write_file’:
> io.c:774: error: too few arguments to function ‘H5Gcreate2’
> io.c:781: error: too few arguments to function ‘H5Gcreate2’
> io.c:880: error: too few arguments to function ‘H5Dcreate2’
> io.c: In function ‘write_header_attributes_in_hdf5’:
> io.c:1005: error: too few arguments to function ‘H5Acreate2’
> io.c:1012: error: too few arguments to function ‘H5Acreate2’
> io.c:1019: error: too few arguments to function ‘H5Acreate2’
> io.c:1027: error: too few arguments to function ‘H5Acreate2’
> io.c:1033: error: too few arguments to function ‘H5Acreate2’
> io.c:1039: error: too few arguments to function ‘H5Acreate2’
> io.c:1045: error: too few arguments to function ‘H5Acreate2’
> io.c:1051: error: too few arguments to function ‘H5Acreate2’
> io.c:1057: error: too few arguments to function ‘H5Acreate2’
> io.c:1063: error: too few arguments to function ‘H5Acreate2’
> io.c:1069: error: too few arguments to function ‘H5Acreate2’
> io.c:1075: error: too few arguments to function ‘H5Acreate2’
> io.c:1081: error: too few arguments to function ‘H5Acreate2’
> io.c:1087: error: too few arguments to function ‘H5Acreate2’
> io.c:1093: error: too few arguments to function ‘H5Acreate2’
> io.c:1099: error: too few arguments to function ‘H5Acreate2’
> io.c:1108: error: too few arguments to function ‘H5Acreate2’
> make: *** [io.o] Error 1
>
>
>
>
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Received on 2011-01-24 22:07:19

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