a problem about hdf5

Hdf-forum archives
1

I have installed hdf5-1.8.4, when I build visit2.0.0, there is something
wrong(as follows), could somebody tell me how to deal with it? Thanks!

silo_hdf5.c:(.text+0x38ac8): undefined reference to `H5Tclose'
/home/xuzhijing/Desktop/visit/silo/lib/libsiloh5.a(silo_hdf5.o): In function
`db_hdf5_GetVarByteLength':
silo_hdf5.c:(.text+0x38c81): undefined reference to `H5Dopen1'
silo_hdf5.c:(.text+0x38c94): undefined reference to `H5Dget_type'
silo_hdf5.c:(.text+0x38cb9): undefined reference to `H5Dget_space'
silo_hdf5.c:(.text+0x38ccf): undefined reference to
`H5Sget_simple_extent_npoints'
silo_hdf5.c:(.text+0x38cdb): undefined reference to `H5Tget_size'
silo_hdf5.c:(.text+0x38d15): undefined reference to `H5Tclose'
silo_hdf5.c:(.text+0x38d20): undefined reference to `H5Sclose'
silo_hdf5.c:(.text+0x38d2b): undefined reference to `H5Dclose'
silo_hdf5.c:(.text+0x38d65): undefined reference to `H5Eauto_is_v2'
silo_hdf5.c:(.text+0x38d82): undefined reference to `H5Eget_auto1'
silo_hdf5.c:(.text+0x38d96): undefined reference to `H5Eset_auto1'
silo_hdf5.c:(.text+0x38da2): undefined reference to `H5Tclose'
silo_hdf5.c:(.text+0x38dae): undefined reference to `H5Sclose'
silo_hdf5.c:(.text+0x38dba): undefined reference to `H5Dclose'
silo_hdf5.c:(.text+0x38ddf): undefined reference to `H5Eset_auto2'
silo_hdf5.c:(.text+0x38e2e): undefined reference to `H5Eget_auto2'
silo_hdf5.c:(.text+0x38e4a): undefined reference to `H5Eset_auto2'
silo_hdf5.c:(.text+0x38e95): undefined reference to `H5Eset_auto1'
/home/xuzhijing/Desktop/visit/silo/lib/libsiloh5.a(silo_hdf5.o): In function
`db_hdf5_GetVarLength':
silo_hdf5.c:(.text+0x38f9a): undefined reference to `H5Dopen1'
silo_hdf5.c:(.text+0x38fac): undefined reference to `H5Dget_space'
silo_hdf5.c:(.text+0x38fbe): undefined reference to
`H5Sget_simple_extent_npoints'
silo_hdf5.c:(.text+0x38fcc): undefined reference to `H5Dclose'
silo_hdf5.c:(.text+0x38fd4): undefined reference to `H5Sclose'
silo_hdf5.c:(.text+0x3900f): undefined reference to `H5Eauto_is_v2'
silo_hdf5.c:(.text+0x3902c): undefined reference to `H5Eget_auto1'
silo_hdf5.c:(.text+0x39040): undefined reference to `H5Eset_auto1'
silo_hdf5.c:(.text+0x3904c): undefined reference to `H5Dclose'
silo_hdf5.c:(.text+0x39058): undefined reference to `H5Sclose'
silo_hdf5.c:(.text+0x3907d): undefined reference to `H5Eset_auto2'
silo_hdf5.c:(.text+0x390d6): undefined reference to `H5Eget_auto2'
silo_hdf5.c:(.text+0x390f2): undefined reference to `H5Eset_auto2'
silo_hdf5.c:(.text+0x3910e): undefined reference to `H5Eset_auto1'
/home/xuzhijing/Desktop/visit/silo/lib/libsiloh5.a(hznwrite.o): In function
`OBSTREAMzlib::OBSTREAMzlib(OBSTREAM*, int, unsigned int, unsigned int)':
hznwrite.cpp:(.text._ZN12OBSTREAMzlibC1EP8OBSTREAMijj[OBSTREAMzlib::OBSTREAMzlib(OBSTREAM*,
int, unsigned int, unsigned int)]+0xdf): undefined reference to
`deflateInit_'
/home/xuzhijing/Desktop/visit/silo/lib/libsiloh5.a(hznwrite.o): In function
`OBSTREAMzlib::encode(int)':
hznwrite.cpp:(.text._ZN12OBSTREAMzlib6encodeEi[OBSTREAMzlib::encode(int)]+0x78):
undefined reference to `deflate'
/home/xuzhijing/Desktop/visit/silo/lib/libsiloh5.a(hznwrite.o): In function
`OBSTREAMzlib::close()':
hznwrite.cpp:(.text._ZN12OBSTREAMzlib5closeEv[OBSTREAMzlib::close()]+0x2f):
undefined reference to `deflateEnd'
/home/xuzhijing/Desktop/visit/silo/lib/libsiloh5.a(hznread.o): In function
`IBSTREAMzlib::IBSTREAMzlib(IBSTREAM*, unsigned int, unsigned int)':
hznread.cpp:(.text._ZN12IBSTREAMzlibC1EP8IBSTREAMjj[IBSTREAMzlib::IBSTREAMzlib(IBSTREAM*,
unsigned int, unsigned int)]+0xe3): undefined reference to `inflateInit_'
/home/xuzhijing/Desktop/visit/silo/lib/libsiloh5.a(hznread.o): In function
`IBSTREAMzlib::decode()':
hznread.cpp:(.text._ZN12IBSTREAMzlib6decodeEv[IBSTREAMzlib::decode()]+0xa7):
undefined reference to `inflate'
hznread.cpp:(.text._ZN12IBSTREAMzlib6decodeEv[IBSTREAMzlib::decode()]+0xc6):
undefined reference to `inflateEnd'

2

here is how i built the hdf with netcdf (you could ignore netcdf part)
please check http://pastebin.com/xtzetmkC .
hope it helps.
winthan

···

On Fri, Apr 23, 2010 at 10:39 AM, 徐致靖 <xuzhijing521@gmail.com> wrote:

I have installed hdf5-1.8.4, when I build visit2.0.0, there is something
wrong(as follows), could somebody tell me how to deal with it? Thanks!

silo_hdf5.c:(.text+0x38ac8): undefined reference to `H5Tclose'
/home/xuzhijing/Desktop/visit/silo/lib/libsiloh5.a(silo_hdf5.o): In
function `db_hdf5_GetVarByteLength':
silo_hdf5.c:(.text+0x38c81): undefined reference to `H5Dopen1'
silo_hdf5.c:(.text+0x38c94): undefined reference to `H5Dget_type'
silo_hdf5.c:(.text+0x38cb9): undefined reference to `H5Dget_space'
silo_hdf5.c:(.text+0x38ccf): undefined reference to
`H5Sget_simple_extent_npoints'
silo_hdf5.c:(.text+0x38cdb): undefined reference to `H5Tget_size'
silo_hdf5.c:(.text+0x38d15): undefined reference to `H5Tclose'
silo_hdf5.c:(.text+0x38d20): undefined reference to `H5Sclose'
silo_hdf5.c:(.text+0x38d2b): undefined reference to `H5Dclose'
silo_hdf5.c:(.text+0x38d65): undefined reference to `H5Eauto_is_v2'
silo_hdf5.c:(.text+0x38d82): undefined reference to `H5Eget_auto1'
silo_hdf5.c:(.text+0x38d96): undefined reference to `H5Eset_auto1'
silo_hdf5.c:(.text+0x38da2): undefined reference to `H5Tclose'
silo_hdf5.c:(.text+0x38dae): undefined reference to `H5Sclose'
silo_hdf5.c:(.text+0x38dba): undefined reference to `H5Dclose'
silo_hdf5.c:(.text+0x38ddf): undefined reference to `H5Eset_auto2'
silo_hdf5.c:(.text+0x38e2e): undefined reference to `H5Eget_auto2'
silo_hdf5.c:(.text+0x38e4a): undefined reference to `H5Eset_auto2'
silo_hdf5.c:(.text+0x38e95): undefined reference to `H5Eset_auto1'
/home/xuzhijing/Desktop/visit/silo/lib/libsiloh5.a(silo_hdf5.o): In
function `db_hdf5_GetVarLength':
silo_hdf5.c:(.text+0x38f9a): undefined reference to `H5Dopen1'
silo_hdf5.c:(.text+0x38fac): undefined reference to `H5Dget_space'
silo_hdf5.c:(.text+0x38fbe): undefined reference to
`H5Sget_simple_extent_npoints'
silo_hdf5.c:(.text+0x38fcc): undefined reference to `H5Dclose'
silo_hdf5.c:(.text+0x38fd4): undefined reference to `H5Sclose'
silo_hdf5.c:(.text+0x3900f): undefined reference to `H5Eauto_is_v2'
silo_hdf5.c:(.text+0x3902c): undefined reference to `H5Eget_auto1'
silo_hdf5.c:(.text+0x39040): undefined reference to `H5Eset_auto1'
silo_hdf5.c:(.text+0x3904c): undefined reference to `H5Dclose'
silo_hdf5.c:(.text+0x39058): undefined reference to `H5Sclose'
silo_hdf5.c:(.text+0x3907d): undefined reference to `H5Eset_auto2'
silo_hdf5.c:(.text+0x390d6): undefined reference to `H5Eget_auto2'
silo_hdf5.c:(.text+0x390f2): undefined reference to `H5Eset_auto2'
silo_hdf5.c:(.text+0x3910e): undefined reference to `H5Eset_auto1'
/home/xuzhijing/Desktop/visit/silo/lib/libsiloh5.a(hznwrite.o): In function
`OBSTREAMzlib::OBSTREAMzlib(OBSTREAM*, int, unsigned int, unsigned int)':
hznwrite.cpp:(.text._ZN12OBSTREAMzlibC1EP8OBSTREAMijj[OBSTREAMzlib::OBSTREAMzlib(OBSTREAM*,
int, unsigned int, unsigned int)]+0xdf): undefined reference to
`deflateInit_'
/home/xuzhijing/Desktop/visit/silo/lib/libsiloh5.a(hznwrite.o): In function
`OBSTREAMzlib::encode(int)':
hznwrite.cpp:(.text._ZN12OBSTREAMzlib6encodeEi[OBSTREAMzlib::encode(int)]+0x78):
undefined reference to `deflate'
/home/xuzhijing/Desktop/visit/silo/lib/libsiloh5.a(hznwrite.o): In function
`OBSTREAMzlib::close()':
hznwrite.cpp:(.text._ZN12OBSTREAMzlib5closeEv[OBSTREAMzlib::close()]+0x2f):
undefined reference to `deflateEnd'
/home/xuzhijing/Desktop/visit/silo/lib/libsiloh5.a(hznread.o): In function
`IBSTREAMzlib::IBSTREAMzlib(IBSTREAM*, unsigned int, unsigned int)':
hznread.cpp:(.text._ZN12IBSTREAMzlibC1EP8IBSTREAMjj[IBSTREAMzlib::IBSTREAMzlib(IBSTREAM*,
unsigned int, unsigned int)]+0xe3): undefined reference to `inflateInit_'
/home/xuzhijing/Desktop/visit/silo/lib/libsiloh5.a(hznread.o): In function
`IBSTREAMzlib::decode()':
hznread.cpp:(.text._ZN12IBSTREAMzlib6decodeEv[IBSTREAMzlib::decode()]+0xa7):
undefined reference to `inflate'
hznread.cpp:(.text._ZN12IBSTREAMzlib6decodeEv[IBSTREAMzlib::decode()]+0xc6):
undefined reference to `inflateEnd'

_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@hdfgroup.org
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org

3

I try it, but it doesn't work

···

2010/4/24 winthan <keshunli@gmail.com>

here is how i built the hdf with netcdf (you could ignore netcdf part)
please check http://pastebin.com/xtzetmkC .
hope it helps.
winthan

On Fri, Apr 23, 2010 at 10:39 AM, 徐致靖 <xuzhijing521@gmail.com> wrote:

I have installed hdf5-1.8.4, when I build visit2.0.0, there is something
wrong(as follows), could somebody tell me how to deal with it? Thanks!

silo_hdf5.c:(.text+0x38ac8): undefined reference to `H5Tclose'
/home/xuzhijing/Desktop/visit/silo/lib/libsiloh5.a(silo_hdf5.o): In
function `db_hdf5_GetVarByteLength':
silo_hdf5.c:(.text+0x38c81): undefined reference to `H5Dopen1'
silo_hdf5.c:(.text+0x38c94): undefined reference to `H5Dget_type'
silo_hdf5.c:(.text+0x38cb9): undefined reference to `H5Dget_space'
silo_hdf5.c:(.text+0x38ccf): undefined reference to
`H5Sget_simple_extent_npoints'
silo_hdf5.c:(.text+0x38cdb): undefined reference to `H5Tget_size'
silo_hdf5.c:(.text+0x38d15): undefined reference to `H5Tclose'
silo_hdf5.c:(.text+0x38d20): undefined reference to `H5Sclose'
silo_hdf5.c:(.text+0x38d2b): undefined reference to `H5Dclose'
silo_hdf5.c:(.text+0x38d65): undefined reference to `H5Eauto_is_v2'
silo_hdf5.c:(.text+0x38d82): undefined reference to `H5Eget_auto1'
silo_hdf5.c:(.text+0x38d96): undefined reference to `H5Eset_auto1'
silo_hdf5.c:(.text+0x38da2): undefined reference to `H5Tclose'
silo_hdf5.c:(.text+0x38dae): undefined reference to `H5Sclose'
silo_hdf5.c:(.text+0x38dba): undefined reference to `H5Dclose'
silo_hdf5.c:(.text+0x38ddf): undefined reference to `H5Eset_auto2'
silo_hdf5.c:(.text+0x38e2e): undefined reference to `H5Eget_auto2'
silo_hdf5.c:(.text+0x38e4a): undefined reference to `H5Eset_auto2'
silo_hdf5.c:(.text+0x38e95): undefined reference to `H5Eset_auto1'
/home/xuzhijing/Desktop/visit/silo/lib/libsiloh5.a(silo_hdf5.o): In
function `db_hdf5_GetVarLength':
silo_hdf5.c:(.text+0x38f9a): undefined reference to `H5Dopen1'
silo_hdf5.c:(.text+0x38fac): undefined reference to `H5Dget_space'
silo_hdf5.c:(.text+0x38fbe): undefined reference to
`H5Sget_simple_extent_npoints'
silo_hdf5.c:(.text+0x38fcc): undefined reference to `H5Dclose'
silo_hdf5.c:(.text+0x38fd4): undefined reference to `H5Sclose'
silo_hdf5.c:(.text+0x3900f): undefined reference to `H5Eauto_is_v2'
silo_hdf5.c:(.text+0x3902c): undefined reference to `H5Eget_auto1'
silo_hdf5.c:(.text+0x39040): undefined reference to `H5Eset_auto1'
silo_hdf5.c:(.text+0x3904c): undefined reference to `H5Dclose'
silo_hdf5.c:(.text+0x39058): undefined reference to `H5Sclose'
silo_hdf5.c:(.text+0x3907d): undefined reference to `H5Eset_auto2'
silo_hdf5.c:(.text+0x390d6): undefined reference to `H5Eget_auto2'
silo_hdf5.c:(.text+0x390f2): undefined reference to `H5Eset_auto2'
silo_hdf5.c:(.text+0x3910e): undefined reference to `H5Eset_auto1'
/home/xuzhijing/Desktop/visit/silo/lib/libsiloh5.a(hznwrite.o): In
function `OBSTREAMzlib::OBSTREAMzlib(OBSTREAM*, int, unsigned int, unsigned
int)':
hznwrite.cpp:(.text._ZN12OBSTREAMzlibC1EP8OBSTREAMijj[OBSTREAMzlib::OBSTREAMzlib(OBSTREAM*,
int, unsigned int, unsigned int)]+0xdf): undefined reference to
`deflateInit_'
/home/xuzhijing/Desktop/visit/silo/lib/libsiloh5.a(hznwrite.o): In
function `OBSTREAMzlib::encode(int)':
hznwrite.cpp:(.text._ZN12OBSTREAMzlib6encodeEi[OBSTREAMzlib::encode(int)]+0x78):
undefined reference to `deflate'
/home/xuzhijing/Desktop/visit/silo/lib/libsiloh5.a(hznwrite.o): In
function `OBSTREAMzlib::close()':
hznwrite.cpp:(.text._ZN12OBSTREAMzlib5closeEv[OBSTREAMzlib::close()]+0x2f):
undefined reference to `deflateEnd'
/home/xuzhijing/Desktop/visit/silo/lib/libsiloh5.a(hznread.o): In function
`IBSTREAMzlib::IBSTREAMzlib(IBSTREAM*, unsigned int, unsigned int)':
hznread.cpp:(.text._ZN12IBSTREAMzlibC1EP8IBSTREAMjj[IBSTREAMzlib::IBSTREAMzlib(IBSTREAM*,
unsigned int, unsigned int)]+0xe3): undefined reference to `inflateInit_'
/home/xuzhijing/Desktop/visit/silo/lib/libsiloh5.a(hznread.o): In function
`IBSTREAMzlib::decode()':
hznread.cpp:(.text._ZN12IBSTREAMzlib6decodeEv[IBSTREAMzlib::decode()]+0xa7):
undefined reference to `inflate'
hznread.cpp:(.text._ZN12IBSTREAMzlib6decodeEv[IBSTREAMzlib::decode()]+0xc6):
undefined reference to `inflateEnd'

_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@hdfgroup.org
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org

_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@hdfgroup.org
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org

4

Have you seen this? http://visitusers.org/index.php?title=VisIt_and_HDF5

-John