Re: Gadget2 on NCSA-Ember

From: Matthew Becker <beckermr_at_uchicago.edu>
Date: Mon, 24 Jan 2011 16:26:48 -0600

This might be type prefixing issue with FFTW. See the gadget-2 manual and
the compile time flag NOTYPEPREFIX_FFTW .

Matt

On Mon, Jan 24, 2011 at 4:18 PM, Agarwal, Shankar <sagarwal_at_ku.edu> wrote:

>
> 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
>
>
>
>
> -----------------------------------------------------------
>
> If you wish to unsubscribe from this mailing, send mail to
> minimalist_at_MPA-Garching.MPG.de<mailto:minimalist_at_MPA-Garching.MPG.de> with
> a subject of: unsubscribe gadget-list
> A web-archive of this mailing list is available here:
> http://www.mpa-garching.mpg.de/gadget/gadget-list
>
>
>
>
> -----------------------------------------------------------
>
> If you wish to unsubscribe from this mailing, send mail to
> minimalist_at_MPA-Garching.MPG.de with a subject of: unsubscribe gadget-list
> A web-archive of this mailing list is available here:
> http://www.mpa-garching.mpg.de/gadget/gadget-list
>
Received on 2011-01-25 00:27:25

This archive was generated by hypermail 2.3.0 : 2022-09-01 14:03:42 CEST