[yt-users] installing yt on Steele

Sat Nov 21 09:41:24 PST 2009

Hi, I am trying to install yt on Steele. When I do "bash install_script.sh", it crashes with H5 warnings and libz.a error.

Any idea?

shankar
KU Cosmology

Building dependencies for H5E.c
H5E.c: in function `H5Eprint':
H5E.c:467: warning: trace info was not inserted
Building dependencies for H5F.c
H5FDmulti.c: in function `H5Pset_fapl_split':
H5FDmulti.c:291: warning: trace info was not inserted
H5FDmulti.c: in function `H5Pset_fapl_multi':
H5FDmulti.c:430: unable to parse `const char * const *memb_name'
H5FDmulti.c: in function `H5Pget_fapl_multi':
H5FDmulti.c:537: warning: trace info was not inserted
H5FDmulti.c: in function `H5Pset_dxpl_multi':
H5FDmulti.c:606: warning: trace info was not inserted
H5FDmulti.c: in function `H5Pget_dxpl_multi':
H5FDmulti.c:658: warning: trace info was not inserted
Building dependencies for H5FDstdio.c
H5FDstdio.c: in function `H5Pset_fapl_stdio':
H5FDstdio.c:272: warning: trace info was not inserted
make[1]: Leaving directory `/autohome/u118/agarwa23/enzo1/src/yt/doc/yt-x86_64/src/hdf5-1.6.8/src'
make[1]: Entering directory `/autohome/u118/agarwa23/enzo1/src/yt/doc/yt-x86_64/src/hdf5-1.6.8/src'
mkdir .libs
mpicc -std=c99 -O3 -Wl,-s -I. -I. -UH5_DEBUG_API -DNDEBUG -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -D_POSIX_SOURCE -D_BSD_SOURCE -c H5Dcontig.c  -fPIC -DPIC -o .libs/H5Dcontig.lo
H5Dcontig.c(497): warning #556: a value of type "const H5D_dxpl_cache_t *" cannot be assigned to an entity of type "H5D_dxpl_cache_t *"
      H5D_BUILD_IO_INFO(&io_info,dset,dxpl_cache,dxpl_id,store);
      ^

mpicc -std=c99 -O3 -Wl,-s -I. -I. -UH5_DEBUG_API -DNDEBUG -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -D_POSIX_SOURCE -
H5Dio.c(3208): warning #556: a value of type "const H5D_dxpl_cache_t *" cannot be assigned to an entity of type "H5D_dxpl_cache_t *"
      io_info->dxpl_cache=dxpl_cache;
                         ^

mpicc -std=c99 -O3 -Wl,-s -I. -I. -UH5_DEBUG_API -DNDEBUG -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -D_POSIX_SOURCE -D_BSD_SOURCE -c H5FD.c  -fPIC -DPIC -o .libs/H5FD.lo
H5FD.c(3670): warning #810: conversion from "void *" to "herr_t={int}" may lose significant bits
  	HGOTO_ERROR(H5E_VFL, H5E_UNSUPPORTED, NULL, "file driver has no `get_vfd_handle' method");
  	^

mpicc -std=c99 -O3 -Wl,-s -I. -I. -UH5_DEBUG_API -DNDEBUG -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -D_POSIX_SOURCE -D_BSD_SOURCE -c H5FDmulti.c  -fPIC -DPIC -o .libs/H5FDmulti.lo
H5FDmulti.c(208): warning #266: function "strlen" declared implicitly
      if (NULL==(x=malloc(strlen(s)+1))) return NULL;
                          ^

H5FDmulti.c(208): warning #167: argument of type "const char *" is incompatible with parameter of type "void *"
      if (NULL==(x=malloc(strlen(s)+1))) return NULL;
                                 ^

H5FDmulti.c(209): warning #266: function "strcpy" declared implicitly
      strcpy(x, s);
      ^

H5FDmulti.c(209): warning #167: argument of type "const char *" is incompatible with parameter of type "void *"
      strcpy(x, s);
                ^

H5FDmulti.c(1924): warning #266: function "memset" declared implicitly
      UNIQUE_MEMBERS(file->fa.memb_map, mt) {
      ^

mpicc -std=c99 -O3 -Wl,-s -I. -I. -UH5_DEBUG_API -DNDEBUG -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -D_POSIX_SOURCE -D_BSD_SOURCE -c H5FDstdio.c  -fPIC -DPIC -o .libs/H5FDstdio.lo
H5FDstdio.c(774): warning #266: function "memset" declared implicitly
          memset(buf, 0, size);
          ^

H5FDstdio.c(800): warning #266: function "memset" declared implicitly
          memset((unsigned char *)buf + size - nbytes, 0, nbytes);
          ^

H5FDstdio.c(815): warning #266: function "memset" declared implicitly
          memset((unsigned char *)buf + n, 0, (size - n));
          ^

mpicc -std=c99 -O3 -Wl,-s -I. -I. -UH5_DEBUG_API -DNDEBUG -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -D_POSIX_SOURCE -D_BSD_SOURCE -c H5Gnode.c  -fPIC -DPIC -o .libs/H5Gnode.lo
H5Gnode.c(1671): warning #188: enumerated type mixed with another type
          udata->type = H5G_get_type(&(sn->entry[loc_idx]), dxpl_id);
                      ^

mpicc -std=c99 -O3 -Wl,-s -I. -I. -UH5_DEBUG_API -DNDEBUG -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -D_POSIX_SOURCE -D_BSD_SOURCE -c H5Gstab.c  -fPIC -DPIC -o .libs/H5Gstab.lo

mpicc -std=c99 -O3 -Wl,-s -I. -I. -UH5_DEBUG_API -DNDEBUG -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -D_POSIX_SOURCE -D_BSD_SOURCE -c H5Obogus.c  -fPIC -DPIC -o .libs/H5Obogus.lo

mpicc -std=c99 -O3 -Wl,-s -I. -I. -UH5_DEBUG_API -DNDEBUG -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -D_POSIX_SOURCE -D_BSD_SOURCE -c H5Spoint.c  -fPIC -DPIC -o .libs/H5Spoint.lo
H5Spoint.c(879): warning #167: argument of type "const hsize_t={unsigned long long} **" is incompatible with parameter of type "const hsize_t={unsigned long long} *"
      if((ret_value=H5S_select_elements(space,op,num_elem,(const hsize_t **)coord))<0)
                                                          ^

mpicc -std=c99 -O3 -Wl,-s -I. -I. -UH5_DEBUG_API -DNDEBUG -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -D_POSIX_SOURCE -D_BSD_SOURCE -c H5Spoint.c -o H5Spoint.o >/dev/null 2>&1
mv -f .libs/H5Spoint.lo H5Spoint.lo
rm -f .libs/H5Sselect.lo
mpicc -std=c99 -O3 -Wl,-s -I. -I. -UH5_DEBUG_API -DNDEBUG -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -D_POSIX_SOURCE -D_BSD_SOURCE -c H5Sselec
mv -f .libs/H5Zszip.lo H5Zszip.lo
rm -fr .libs/libhdf5.la .libs/libhdf5.* .libs/libhdf5.*
mpicc -shared  H5.lo H5A.lo H5AC.lo H5B.lo H5Bcache.lo H5C.lo H5D.lo H5Dcontig.lo H5Dcompact.lo H5Defl.lo H5Dio.lo H5Distore.lo H5Dmpio.lo H5Dselect.lo H5Dtest.lo H5E.lo H5F.lo H5Fdbg.lo H5Fmount.lo H5Fsfile.lo H5Fsuper.lo H5FD.lo H5FDcore.lo H5FDfamily.lo H5FDlog.lo H5FDmpi.lo H5FDmpio.lo H5FDmpiposix.lo H5FDmulti.lo H5FDsec2.lo H5FDstdio.lo H5FL.lo H5FO.lo H5FS.lo H5G.lo H5Gent.lo H5Gname.lo H5Gnode.lo H5Gstab.lo H5Gtest.lo H5Gtraverse.lo H5HG.lo H5HGdbg.lo H5HL.lo H5HLdbg.lo H5HP.lo H5I.lo H5MF.lo H5MM.lo H5O.lo H5Oattr.lo H5Obogus.lo H5Ocache.lo H5Ocont.lo H5Odtype.lo H5Oefl.lo H5Ofill.lo H5Olayout.lo H5Omtime.lo H5Oname.lo H5Onull.lo H5Opline.lo H5Osdspace.lo H5Oshared.lo H5Ostab.lo H5P.lo H5Pdcpl.lo H5Pdxpl.lo H5Pfapl.lo H5Pfcpl.lo H5Ptest.lo H5R.lo H5RC.lo H5RS.lo H5S.lo H5Sall.lo H5Shyper.lo H5Smpio.lo H5Snone.lo H5Spoint.lo H5Sselect.lo H5Stest.lo H5SL.lo H5ST.lo H5T.lo H5Tarray.lo H5Tbit.lo H5Tcommit.lo H5Tcompound.lo H5Tconv.lo H5Tcset.lo H5Tenum.lo H5Tfields.lo H5Tfixed.lo H5Tfloat.lo H5Tinit.lo H5Tnative.lo H5Toffset.lo H5Topaque.lo H5Torder.lo H5Tpad.lo H5Tprecis.lo H5Tstrpad.lo H5Tvlen.lo H5TS.lo H5V.lo H5Z.lo H5Zdeflate.lo H5Zfletcher32.lo H5Zshuffle.lo H5Zszip.lo  -Wl,--rpath -Wl,/home/ba01/u118/agarwa23/enzo1/src/yt/doc/yt-x86_64/lib64/ -Wl,--rpath -Wl,/home/ba01/u118/agarwa23/enzo1/src/yt/doc/yt-x86_64/lib/  -L/home/ba01/u118/agarwa23/enzo1/src/yt/doc/yt-x86_64/lib/ -L/home/ba01/u118/agarwa23/enzo1/src/yt/doc/yt-x86_64/lib64/ -lz -lm  -Wl,-s -Wl,-soname -Wl,libhdf5.so.0 -o .libs/libhdf5.so.0.0.0
ld: /home/ba01/u118/agarwa23/enzo1/src/yt/doc/yt-x86_64/lib//libz.a(compress.o): relocation R_X86_64_32 against `a local symbol' can not be used when making a shared object; recompile with -fPIC
/home/ba01/u118/agarwa23/enzo1/src/yt/doc/yt-x86_64/lib//libz.a: could not read symbols: Bad value
make[1]: *** [libhdf5.la] Error 1
make[1]: Leaving directory `/autohome/u118/agarwa23/enzo1/src/yt/doc/yt-x86_64/src/hdf5-1.6.8/src'
make: *** [install] Error 1