RE: Gadget2 on NCSA-Ember

From: Agarwal, Shankar <sagarwal_at_ku.edu>
Date: Mon, 24 Jan 2011 22:18:10 +0000

Hi all,

-DH5_USE_16_API together with fftw/2.1.5 compiled Gadget2 pretty well, except a few warnings which I think can be safely ignored:

gcc -lmpi -O3 -Wall -DPERIODIC -DUNEQUALSOFTENINGS -DPEANOHILBERT -DWALLCLOCK -DPMGRID=128 -DSYNCHRONIZATION -DHAVE_HDF5 -DH5_USE_16_API -I/usr/apps/math/gsl/gnu/1.14/include -I/usr/apps/math/fftw/gnu/2.1.5/include -I/usr/apps/hdf/hdf5/v185-patch1/include -c -o allocate.o allocate.c
allocate.c: In function ‘allocate_memory’:
allocate.c:118: warning: format ‘%d’ expects type ‘int’, but argument 3 has type ‘long unsigned int’
allocate.c:127: warning: format ‘%d’ expects type ‘int’, but argument 3 has type ‘long unsigned int’
allocate.c:133: warning: format ‘%d’ expects type ‘int’, but argument 3 has type ‘long unsigned int’


But I still get this error:

[sagarwal_at_ember Gadget2]$ ./Gadget2
./Gadget2: error while loading shared libraries: libsrfftw_mpi.so.2: cannot open shared object file: No such file or directory


I guess it is something to do with the PATH ? Let me know.

-Shankar

________________________________________
From: Matthew Becker [beckermr_at_uchicago.edu]
Sent: Monday, January 24, 2011 2:33 PM
To: Gadget General Discussion
Subject: Re: [gadget-list] Gadget2 on NCSA-Ember

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<mailto: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 23:18:14

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