[yt-users] installing yt on Steele
Agarwal, Shankar
sagarwal at ku.edu
Sat Nov 21 10:05:49 PST 2009
Hi Matt, so i did...
[agarwa23 at tg-steele ~]$ module list
Currently Loaded Modulefiles:
1) intel64/11.1.038 2) mpich-intel64/11.1.038 3) java/1.6.0_14 4) mpich2-intel64/11.1.038 5) hdf5-1.8.3/intel-parallel
I can load gnu modules as well. But just wanted to know if it is necessary to remove intel and mpi modules ? I am currently running enzo on 24 processors. Will that get affected ? Also, will loading gnu affect my enzo simulation?
shankar
-----Original Message-----
From: yt-users-bounces at lists.spacepope.org on behalf of Matthew Turk
Sent: Sat 11/21/2009 11:49 AM
To: Discussion of the yt analysis package
Subject: Re: [yt-users] installing yt on Steele
Hi Shankar,
So what's going on here is a couple things.
libz has been installed by the yt installer script, but for some
reason has not been compiled as a shared library. The yt installer
script does ask libz to compile as shared, but it seems that this
request was not honored. Unfortunately, for the very reasons you see,
we want it compiled as shared.
The second thing seems to be that it's using mpicc -- according to the
Steele operating guide
(http://www.rcac.purdue.edu/userinfo/resources/steele/userguide.cfm#compile_compilers
) you probably have an mpi module loaded, and it might also be trying
to compile with intel or pgi or one of those compiler sets. For now,
the installation procedure for non-GNU is tricky and requires some
manual intervention.
I think that you might be able to solve the problem by swapping out
the pgi or intel modules for the gnu module (as described in that
linked user guide), *unloading* any MPI modules that might be loaded
(check via module list), wiping the entire yt-x86_64 directory and
re-running the install script. You're early enough in that this
shouldn't double up on a lot of time in compilation.
If this still causes problems, could you send the part of the log file
dealing with the libz installation, as well as the HDF5?
Additionally, if this solution works, I will add it as a note to the
install_script.sh file as well as the documentation. This is the
solution we had to use on Ranger for just this very reason.
Good luck, and let us know!
-Matt
On Sat, Nov 21, 2009 at 9:41 AM, Agarwal, Shankar <sagarwal at ku.edu> wrote:
> 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 H5
> Tfixed.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
>
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