Gadget compilations problems with hdf5

From: Andreu Coll i Pla <andreu.fanera_at_gmail.com>
Date: Wed, 9 May 2012 19:15:14 +0200

Hello all,

I'm starting with Gadged2, currently I have started using a new IC code,
the makegalaxy. The outputs of this code are in hdf5 format so I need that
option enabled in Gadget2. Without this option the program works with now
problem.

My problems appear when i do make.

I installed the HDF5 1.8.7 version, the developer file using the yum
repository. I know that is not compatible, but i read that if you add
-DH5_USE_16_API to the CFLAGS then it works. I actually add this to the
Gadget makefile CFLAGS. This make the simulation to run a bit more before
having problems.
The actual problem is with the headers, that's the output:

io.o: In function `write_header_attributes_in_hdf5':
/home/extragalactic/owasco/acoll/Programes/Gadget-2.0.7/firsts_simulations/gasgalaxy/Gadget/io.c:1003:
undefined reference to `H5Screate'
/home/extragalactic/owasco/acoll/Programes/Gadget-2.0.7/firsts_simulations/gasgalaxy/Gadget/io.c:1004:
undefined reference to `H5Sset_extent_simple'
/home/extragalactic/owasco/acoll/Programes/Gadget-2.0.7/firsts_simulations/gasgalaxy/Gadget/io.c:1005:
undefined reference to `H5open'
/home/extragalactic/owasco/acoll/Programes/Gadget-2.0.7/firsts_simulations/gasgalaxy/Gadget/io.c:1005:
undefined reference to `H5T_NATIVE_INT_g'

...(more and more)

/home/extragalactic/owasco/acoll/Programes/Gadget-2.0.7/firsts_simulations/gasgalaxy/Gadget/read_ic.c:306:
undefined reference to `H5Fopen'
/home/extragalactic/owasco/acoll/Programes/Gadget-2.0.7/firsts_simulations/gasgalaxy/Gadget/read_ic.c:313:
undefined reference to `H5Gopen1'
read_ic.o: In function `read_header_attributes_in_hdf5':
/home/extragalactic/owasco/acoll/Programes/Gadget-2.0.7/firsts_simulations/gasgalaxy/Gadget/read_ic.c:802:
undefined reference to `H5Fclose'
collect2: ld returned 1 exit status
make: *** [Gadget2] Error 1

My makefile looks like:

ifeq ($(SYSTIPE),"OWASCO")
CC = mpicc
OPTIMIZE = -O3 -Wall
GSL_INCL = -I/usr/local/include
GSL_LIBS = -L/usr/local/bin
FFTW_INCL= -I/usr/libold/include
FFTW_LIBS= -L/usr/libold/lib
MPICHLIB = -I/usr/lib64/mpich2/lib
HDF5INCL = -I/usr/lib64/include
HDF5LIB = -L/usr/lib64/lib -lhdf5 -lz -
endif
...
CFLAGS = $(OPTIONS) $(GSL_INCL) $(FFTW_INCL) $(HDF5INCL) -DH5_USE_16_API
....

Does anyone could help me?

Thank you very much in advance!

Andreu
Received on 2012-05-09 19:15:30

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