Re: hdf5-1.9.145 & fftw

From: Desika Narayanan <dnarayan_at_haverford.edu>
Date: Mon, 3 Mar 2014 09:25:11 -0500

Hi All,

This might be outdated, but I've found it useful for ensuring that I'm
using the correct libraries:

http://www.hpcadvisorycouncil.com/pdf/GADGET-2_Best_Practices.pdf

cheers,
desika


On Sun, Mar 2, 2014 at 11:36 PM, Antonio Bibiano <antbbn_at_gmail.com> wrote:

>
> fftw3 is not an option, you must use version fftw2 with gadget2.
>
> Instead you can use the new HDF5 libraries with gadget2 but you need
> to enable the old api interface by adding this line to the makefile:
>
> OPT += -DH5_USE_16_API
>
> hope this helps,
>
> Antonio Bibiano
>
> 2014-03-03 15:26 GMT+11:00 yueh wang <cw5b_at_msn.com>:
> > Hi,
> >
> > We have problems in compiling the Gadget II in our personal Ubuntu
> > computers.
> > Which HDF and FFTW version does Gadget II work with?
> >
> > hdf5-1.9.145 does not work.
> > fftw3 also does not work.
> > However, when HDF is not linked, fftw-2.1.5.tar.gz can work.
> >
> > Thanks for your help.
> >
> > Chih-Yueh Wang
> >
> > -----------------
> >
> > io.c: In function ‘get_particles_in_block’:
> > io.c:467:39: warning: variable ‘nstars’ set but not used
> > [-Wunused-but-set-variable]
> > int i, nall, ntot_withmasses, ngas, nstars;
> >
> > io.c: In function ‘write_file’:
> > io.c:774:4: error: too few arguments to function ‘H5Gcreate2’
> > hdf5_headergrp = H5Gcreate(hdf5_file, "/Header", 0);
> > H5Gpublic.h:75:14: note: declared here
> > H5_DLL hid_t H5Gcreate2(hid_t loc_id, const char *name, hid_t
> > lcpl_id, hid_t gcpl_id, hid_t gapl_id);
> >
> > io.c:781:5: error: too few arguments to function ‘H5Gcreate2
> > hdf5_grp[type] = H5Gcreate(hdf5_file, buf, 0)
> > H5Gpublic.h:75:14: note: declared here
> > H5_DLL hid_t H5Gcreate2(hid_t loc_id, const char *name, hid_t
> > lcpl_id, hid_t gcpl_id, hid_t gapl_id);
> >
> > io.c:880:11: error: too few arguments to function ‘H5Dcreate2’
> > H5Dcreate(hdf5_grp[type], buf, hdf5_datatype, hdf5_dataspace_in_file,
> > H5P_DEFAULT);
> > H5Dpublic.h:119:14: note: declared here
> > H5_DLL hid_t H5Dcreate2(hid_t loc_id, const char *name, hid_t type_id,
> > hid_t space_id, hid_t lcpl_id, hid_t dcpl_id, hid_t dapl_id);
> > io.c:685:10: warning: variable ‘hdf5_status’ set but not used
> > [-Wunused-but-set-variable]
> > herr_t hdf5_status;
> > io.c:675:24: warning: variable ‘ntask’ set but not used
> > [-Wunused-but-set-variable]
> > int n_for_this_task, ntask, n, p, pc, offset = 0, task;
> >
> >
> > io.c: In function ‘write_header_attributes_in_hdf5’:
> > too few arguments to function ‘H5Acreate2’
> > H5Acreate2 :
> > H5Apublic.h:44:16: note: declared here
> > H5_DLL hid_t H5Acreate2(hid_t loc_id, const char *attr_name, hid_t
> > type_id,
> > hid_t space_id, hid_t acpl_id, hid_t aapl_id);
> >
> > io.c:1005:3: error: too few arguments to function ‘H5Acreate2’
> > hdf5_attribute = H5Acreate(handle, "NumPart_ThisFile", H5T_NATIVE_INT,
> > hdf5_dataspace, H5P_DEFAULT);
> >
> > io.c:1012:3: error: too few arguments to function ‘H5Acreate2’
> > hdf5_attribute = H5Acreate(handle, "NumPart_Total", H5T_NATIVE_UINT,
> > hdf5_dataspace, H5P_DEFAULT);
> >
> > io.c:1019:3: error: too few arguments to function ‘H5Acreate2’
> > hdf5_attribute = H5Acreate(handle, "NumPart_Total_HighWord",
> > H5T_NATIVE_UINT, hdf5_dataspace, H5P_DEFAULT);
> >
> > io.c:1027:3: error: too few arguments to function ‘H5Acreate2’
> > hdf5_attribute = H5Acreate(handle, "MassTable", H5T_NATIVE_DOUBLE,
> > hdf5_dataspace, H5P_DEFAULT);
> >
> > io.c:1033:3: error: too few arguments to function ‘H5Acreate2’
> > hdf5_attribute = H5Acreate(handle, "Time", H5T_NATIVE_DOUBLE,
> > hdf5_dataspace, H5P_DEFAULT);
> >
> > io.c:1039:3: error: too few arguments to function ‘H5Acreate2’
> > hdf5_attribute = H5Acreate(handle, "Redshift", H5T_NATIVE_DOUBLE,
> > hdf5_dataspace, H5P_DEFAULT);
> >
> > io.c:1045:3: error: too few arguments to function ‘H5Acreate2’
> > hdf5_attribute = H5Acreate(handle, "BoxSize", H5T_NATIVE_DOUBLE,
> > hdf5_dataspace, H5P_DEFAULT);
> >
> > io.c:1051:3: error: too few arguments to function ‘H5Acreate2’
> > hdf5_attribute = H5Acreate(handle, "NumFilesPerSnapshot",
> H5T_NATIVE_INT,
> > hdf5_dataspace, H5P_DEFAULT);
> >
> > io.c:1057:3: error: too few arguments to function ‘H5Acreate2’
> > hdf5_attribute = H5Acreate(handle, "Omega0", H5T_NATIVE_DOUBLE,
> > hdf5_dataspace, H5P_DEFAULT);
> >
> > io.c:1063:3: error: too few arguments to function ‘H5Acreate2’
> > hdf5_attribute = H5Acreate(handle, "OmegaLambda", H5T_NATIVE_DOUBLE,
> > hdf5_dataspace, H5P_DEFAULT);
> >
> > io.c:1069:3: error: too few arguments to function ‘H5Acreate2'
> > hdf5_attribute = H5Acreate(handle, "HubbleParam", H5T_NATIVE_DOUBLE,
> > hdf5_dataspace, H5P_DEFAULT);
> >
> > io.c:1075:3: error: too few arguments to function ‘H5Acreate2’
> > hdf5_attribute = H5Acreate(handle, "Flag_Sfr", H5T_NATIVE_INT,
> > hdf5_dataspace, H5P_DEFAULT);
> >
> > io.c:1081:3: error: too few arguments to function ‘H5Acreate2’
> > hdf5_attribute = H5Acreate(handle, "Flag_Cooling", H5T_NATIVE_INT,
> > hdf5_dataspace, H5P_DEFAULT);
> >
> > io.c:1087:3: error: too few arguments to function ‘H5Acreate2’
> > hdf5_attribute = H5Acreate(handle, "Flag_StellarAge", H5T_NATIVE_INT,
> > hdf5_dataspace, H5P_DEFAULT);
> >
> > io.c:1093:3: error: too few arguments to function ‘H5Acreate2’
> > hdf5_attribute = H5Acreate(handle, "Flag_Metals", H5T_NATIVE_INT,
> > hdf5_dataspace, H5P_DEFAULT);
> >
> > io.c:1099:3: error: too few arguments to function ‘H5Acreate2’
> > hdf5_attribute = H5Acreate(handle, "Flag_Feedback", H5T_NATIVE_INT,
> > hdf5_dataspace, H5P_DEFAULT);
> >
> > io.c:1108:3: error: too few arguments to function ‘H5Acreate2’
> > hdf5_attribute = H5Acreate(handle, "Flag_Entropy_ICs",
> H5T_NATIVE_UINT,
> > hdf5_dataspace, H5P_DEFAULT);
> >
> >
> >
> >
> >
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>
>
>
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Received on 2014-03-03 15:25:52

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