Re: HDF5 error with gmt 4.5.12
Joaquim Luis <[email protected]> Fri, 15 Aug 2014 19:39:32 -0400
| Newsgroups | gmane.comp.gis.gmt.user |
|---|---|
| Message-ID | <[email protected]> |
--Apple-Mail-5E45EBD2-475B-43A9-9F72-A9B6731F5073 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable Gery, That warning from HDF essentially means that you are screwed. The computer w= ill blow, or at least you'll get a crash. The HDF version used to link GDAL a= nd the one at use must be exactly the same. Still, on the land of opinions, Cygwin sucks compared with with MinGW where y= ou can just use the, way faster, GMT5 Win binaries provided by us.=20 Sent from my iPadiola > On 15/08/2014, at 12:57, "Gery ." <[email protected]> wrote: >=20 > Sorry for the last noisy message, but things were smooth finally, the solu= tion was to install without gdal. Now things work, but I received this messa= ge about HDF5: >=20 > -----------------------------------------------------------=E2=80=8B > $ pscoast -R-71.2/-70.9/42.25/42.45 -JM6.0 -Ba0.05f0.01SWen -Ia -Na -W3 -K= > ps >=20 > Warning! ***HDF5 library version mismatched error*** >=20 > The HDF5 header files used to compile this application do not match >=20 > the version used by the HDF5 library to which this application is linked. >=20 > Data corruption or segmentation faults may occur if the application contin= ues. >=20 > This can happen when an application was compiled by one version of HDF5 bu= t >=20 > linked with a different version of static or shared HDF5 library. >=20 > You should recompile the application or check your shared library related >=20 > settings such as 'LD_LIBRARY_PATH'. >=20 > You can, at your own risk, disable this warning by setting the environment= >=20 > variable 'HDF5_DISABLE_VERSION_CHECK' to a value of '1'. >=20 > Setting it to 2 or higher will suppress the warning messages totally. >=20 > Headers are 1.8.12, library is 1.8.13 >=20 > SUMMARY OF THE HDF5 CONFIGURATION >=20 > =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D >=20 > General Information: >=20 > ------------------- >=20 > HDF5 Version: 1.8.13 >=20 > Configured on: Wed Jun 4 15:04:57 CEST 2014 >=20 > Configured by: marco@GE-MATZERI-EU >=20 > Configure mode: production >=20 > Host system: i686-pc-cygwin >=20 > Uname information: CYGWIN_NT-6.1-WOW64 GE-MATZERI-EU 1.7.30(0.272/5/3) 201= 4-05-23 10:36 i686 Cygwin >=20 > Byte sex: little-endian >=20 > Libraries: shared >=20 > Installation point: /usr >=20 > Compiling Options: >=20 > ------------------ >=20 > Compilation Mode: production >=20 > C Compiler: /usr/bin/gcc >=20 > CFLAGS: -ggdb -O2 -pipe -Wimplicit-function-declaration -fdebug-prefix-map= =3D/pub/devel/hdf5/hdf5-1.8.13-1/ build=3D/usr/src/debug/hdf5-1.8.13-1 -fdeb= ug-prefix-map=3D/pub/devel/hdf5/hdf5-1.8.13-1/src/hdf5-1.8.13=3D/usr/src/deb= ug/hdf5-1.8.13-1 >=20 > H5_CFLAGS: -std=3Dc99 -pedantic -Wall -Wextra -Wundef -Wshadow -Wpointer-a= rith -Wbad-function-cast -Wcast-qual -Wcast-align -Wwrite-strings -Wconversi= on -Waggregate-return -Wstrict-prototypes -Wmissing-prototypes -Wmissing-dec= larations -Wre dundant-decls -Wnested-externs -Winline -Wfloat-equal -Wmissi= ng-format-attribute -Wmissing-noreturn -Wpacked -Wdisabled-optimizati on -Wf= ormat=3D2 -Wunreachable-code -Wendif-labels -Wdeclaration-after-statement -W= old-style-definition -Winvalid-pch -Wvariadic-macr os -Winit-self -Wmissing-= include-dirs -Wswitch-default -Wswitch-enum -Wunused-macros -Wunsafe-loop-op= timizations -Wc++-compat -Wst rict-overflow -Wlogical-op -Wlarger-than=3D204= 8 -Wvla -Wsync-nand -Wframe-larger-than=3D16384 -Wpacked-bitfield-compat -Ws= trict-overfl ow=3D5 -Wjump-misses-init -Wunsuffixed-float-constants -Wdouble= -promotion -Wsuggest-attribute=3Dconst -Wtrampolines -Wstack-usage=3D8192 -W= vector-operation-performance -Wsuggest-attribute=3Dpure -Wsuggest-attribute=3D= noreturn -Wsuggest-attribute=3Dformat -O3 -fomit-frame- pointer -finline-fun= ctions >=20 > AM_CFLAGS: >=20 > CPPFLAGS: >=20 > H5_CPPFLAGS: -DNDEBUG -UH5_DEBUG_API >=20 > AM_CPPFLAGS: >=20 > Shared C Library: yes >=20 > Static C Library: no >=20 > Statically Linked Executables: no >=20 > LDFLAGS: >=20 > H5_LDFLAGS: -no-undefined >=20 > AM_LDFLAGS: >=20 > Extra libraries: -lz -ldl -lm >=20 > Archiver: ar >=20 > Ranlib: ranlib >=20 > Debugged Packages: >=20 > API Tracing: no >=20 > Languages: >=20 > ---------- >=20 > Fortran: no >=20 > C++: yes >=20 > C++ Compiler: /usr/bin/g++ >=20 > C++ Flags: -ggdb -O2 -pipe -fdebug-prefix-map=3D/pub/devel/hdf5/hdf5-1.8.1= 3-1/build=3D/usr/src/debug/hdf5-1.8.13 -1 -fdebug-prefix-map=3D/pub/devel/hd= f5/hdf5-1.8.13-1/src/hdf5-1.8.13=3D/usr/src/debug/hdf5-1.8.13-1 >=20 > H5 C++ Flags: >=20 > AM C++ Flags: >=20 > Shared C++ Library: yes >=20 > Static C++ Library: no >=20 > Features: >=20 > --------- >=20 > Parallel HDF5: no >=20 > High Level library: yes >=20 > Threadsafety: no >=20 > Default API Mapping: v18 >=20 > With Deprecated Public Symbols: yes >=20 > I/O filters (external): deflate(zlib) >=20 > I/O filters (internal): shuffle,fletcher32,nbit,scaleoffset >=20 > MPE: no >=20 > Direct VFD: yes >=20 > dmalloc: no >=20 > Clear file buffers before write: yes >=20 > Using memory checker: no >=20 > Function Stack Tracing: no >=20 > Strict File Format Checks: no >=20 > Optimization Instrumentation: no >=20 > Large File Support (LFS): yes >=20 > Bye... >=20 > Aborted (core dumped) >=20 > ----------------------------------------------------------- >=20 > I have the latest Cygwin 32-bit version. Which HDF5 version should I use? t= his Cygwin comes with hdf5 1.8.13-1, netcdf 4.3.2-1 and zlib 1.2.8-1. >=20 > Any ideas?? thank.. >=20 > Gery >=20 > Mailing list for GMT discussions of all kinds. If you are not sure you hav= e found a bug, discuss it here first. To formally report bugs or request fea= tures, please register and add New Issue on gmt.soest.hawaii.edu To unsubscr= ibe, send the message "signoff gmt-help" to [email protected] Note: g= mt-help will become obsolete on Sept 1, 2014 - please use forum on gmt.soest= .hawaii.edu instead. Mailing list for GMT discussions of all kinds. If you are not sure you have found a bug, discuss it here first. To formally report bugs or request features, please register and add New Issue on gmt.soest.hawaii.edu To unsubscribe, send the message "signoff gmt-help" to [email protected] Note: gmt-help will become obsolete on Sept 1, 2014 - please use forum on gmt.soest.hawaii.edu instead. --Apple-Mail-5E45EBD2-475B-43A9-9F72-A9B6731F5073 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: quoted-printable <html><head><meta http-equiv=3D"content-type" content=3D"text/html; charset=3D= utf-8"></head><body dir=3D"auto"><div>Gery,</div><div><br></div><div>That wa= rning from HDF essentially means that you are screwed. The computer will blo= w, or at least you'll get a crash. The HDF version used to link GDAL and the= one at use must be exactly the same.</div><div>Still, on the land of opinio= ns, Cygwin sucks compared with with MinGW where you can just use the, way fa= ster, GMT5 Win binaries provided by us. <br><br>Sent from my iPadiola</= div><div><br>On 15/08/2014, at 12:57, "Gery ." <<a href=3D"mailto:gamejih= [email protected]">[email protected]</a>> wrote:<br><br></div><blockquot= e type=3D"cite"><div> <meta name=3D"generator" content=3D"Windows Mail 17.5.9600.20573"> <style data-externalstyle=3D"true"><!-- p.MsoListParagraph, li.MsoListParagraph, div.MsoListParagraph { margin-top:0in; margin-right:0in; margin-bottom:0in; margin-left:.5in; margin-bottom:.0001pt; } p.MsoNormal, li.MsoNormal, div.MsoNormal { margin:0in; margin-bottom:.0001pt; } p.MsoListParagraphCxSpFirst, li.MsoListParagraphCxSpFirst, div.MsoListParagr= aphCxSpFirst,=20 p.MsoListParagraphCxSpMiddle, li.MsoListParagraphCxSpMiddle, div.MsoListPara= graphCxSpMiddle,=20 p.MsoListParagraphCxSpLast, li.MsoListParagraphCxSpLast, div.MsoListParagrap= hCxSpLast { margin-top:0in; margin-right:0in; margin-bottom:0in; margin-left:.5in; margin-bottom:.0001pt; line-height:115%; } --></style> <div data-externalstyle=3D"false" dir=3D"ltr" style=3D"font-family: 'Calibri= ', 'Segoe UI', 'Meiryo', 'Microsoft YaHei UI', 'Microsoft JhengHei UI', 'Mal= gun Gothic', 'sans-serif';font-size:12pt;"><div>Sorry for the last noisy mes= sage, but things were smooth finally, the solution was to install without gd= al. Now things work, but I received this message about HDF5:</div><div><br><= /div><div>-----------------------------------------------------------=E2=80=8B= </div><div><p>$ pscoast -R-71.2/-70.9/42.25/42.45 -JM6.0 -Ba0.05f0.01SWen -I= a -Na -W3 -K > ps</p><p>Warning! ***HDF5 library version mismatched error= ***</p></div><div> <p>The HDF5 header files used to compile this application do not match</p> <p>the version used by the HDF5 library to which this application is linked.= </p> <p>Data corruption or segmentation faults may occur if the application conti= nues.</p> <p>This can happen when an application was compiled by one version of HDF5 b= ut</p> <p>linked with a different version of static or shared HDF5 library.</p> <p>You should recompile the application or check your shared library related= </p> <p>settings such as 'LD_LIBRARY_PATH'.</p> <p>You can, at your own risk, disable this warning by setting the environmen= t</p> <p>variable 'HDF5_DISABLE_VERSION_CHECK' to a value of '1'.</p> <p>Setting it to 2 or higher will suppress the warning messages totally.</p>= <p>Headers are 1.8.12, library is 1.8.13</p> <p> SUMMARY OF THE HDF5 CONFIGURATION</p> <p> =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D</p> <p>General Information:</p> <p>-------------------</p> <p> HDF5 Version: 1.8.13</p> <p> Configured on: Wed Jun 4 15:04:57 CEST 2014</p> <p> Configured by: marco@GE-MATZERI-EU</p> <p> Configure mode: production</p> <p> Host system: i686-pc-cygwin</p> <p> Uname information: CYGWIN_NT-6.1-WOW64 GE-MATZERI-EU 1.7.30= (0.272/5/3) 2014-05-23 10:36 i686 Cygwin</p> <p> Byte sex: little-endian</p> <p> Libraries: shared</p> <p> Installation point: /usr</p> <p>Compiling Options:</p> <p>------------------</p> <p> Compilation Mode: production</p> <p> C Compiler: /usr/bin/gcc</p> <p> CFLAGS: -ggdb -O2 -pipe -Wimplicit-function-decl= aration -fdebug-prefix-map=3D/pub/devel/hdf5/hdf5-1.8.13-1/ = build=3D/usr/src/debug/hdf5-1.8.13-1 -fdebug-prefix-map=3D/pub/devel/hdf5/= hdf5-1.8.13-1/src/hdf5-1.8.13=3D/usr/src/debug/hdf5-1.8.13-1</p> <p> H5_CFLAGS: -std=3Dc99 -pedantic -Wall -Wextra -Wund= ef -Wshadow -Wpointer-arith -Wbad-function-cast -Wcast-qual = -Wcast-align -Wwrite-strings -Wconversion -Waggregate-return -Wstrict-pro= totypes -Wmissing-prototypes -Wmissing-declarations -Wre d= undant-decls -Wnested-externs -Winline -Wfloat-equal -Wmissing-format-attrib= ute -Wmissing-noreturn -Wpacked -Wdisabled-optimizati on -= Wformat=3D2 -Wunreachable-code -Wendif-labels -Wdeclaration-after-statement -= Wold-style-definition -Winvalid-pch -Wvariadic-macr os -Wi= nit-self -Wmissing-include-dirs -Wswitch-default -Wswitch-enum -Wunused-macr= os -Wunsafe-loop-optimizations -Wc++-compat -Wst rict-over= flow -Wlogical-op -Wlarger-than=3D2048 -Wvla -Wsync-nand -Wframe-larger-than= =3D16384 -Wpacked-bitfield-compat -Wstrict-overfl ow=3D5 -= Wjump-misses-init -Wunsuffixed-float-constants -Wdouble-promotion -Wsuggest-= attribute=3Dconst -Wtrampolines -Wstack-usage=3D8192 -Wve= ctor-operation-performance -Wsuggest-attribute=3Dpure -Wsuggest-attribute=3D= noreturn -Wsuggest-attribute=3Dformat -O3 -fomit-frame- po= inter -finline-functions</p> <p> AM_CFLAGS:</p> <p> CPPFLAGS:</p> <p> H5_CPPFLAGS: -DNDEBUG -UH5_DEBUG_API</p> <p> AM_CPPFLAGS:</p> <p> Shared C Library: yes</p> <p> Static C Library: no</p> <p> Statically Linked Executables: no</p> <p> LDFLAGS:</p> <p> H5_LDFLAGS: -no-undefined</p> <p> AM_LDFLAGS:</p> <p> Extra libraries: -lz -ldl -lm</p> <p> Archiver: ar</p> <p> Ranlib: ranlib</p> <p> Debugged Packages:</p> <p> API Tracing: no</p> <p>Languages:</p> <p>----------</p> <p> Fortran: no</p> <p> C++: yes</p> <p> C++ Compiler: /usr/bin/g++</p> <p> C++ Flags: -ggdb -O2 -pipe -fdebug-prefix-map=3D/pu= b/devel/hdf5/hdf5-1.8.13-1/build=3D/usr/src/debug/hdf5-1.8.13 = -1 -fdebug-prefix-map=3D/pub/devel/hdf5/hdf5-1.8.13-1/src/hdf5-1.8.13=3D= /usr/src/debug/hdf5-1.8.13-1</p> <p> H5 C++ Flags:</p> <p> AM C++ Flags:</p> <p> Shared C++ Library: yes</p> <p> Static C++ Library: no</p> <p>Features:</p> <p>---------</p> <p> Parallel HDF5: no</p> <p> High Level library: yes</p> <p> Threadsafety: no</p> <p> Default API Mapping: v18</p> <p> With Deprecated Public Symbols: yes</p> <p> I/O filters (external): deflate(zlib)</p> <p> I/O filters (internal): shuffle,fletcher32,nbit,scaleoffset</p> <p> MPE: no</p> <p> Direct VFD: yes</p> <p> dmalloc: no</p> <p>Clear file buffers before write: yes</p> <p> Using memory checker: no</p> <p> Function Stack Tracing: no</p> <p> Strict File Format Checks: no</p> <p> Optimization Instrumentation: no</p> <p> Large File Support (LFS): yes</p> <p>Bye...</p> <p>Aborted (core dumped)</p><p>---------------------------------------------= --------------</p></div><div>I have the latest Cygwin 32-bit version. Which H= DF5 version should I use? this Cygwin comes with hdf5 1.8.13-1, netcdf 4.3.2= -1 and zlib 1.2.8-1.</div><div>= <br></div><div>Any ideas?? thank..</div><div><br></div><div>Gery</div><div><= br></div> </div> Mailing list for GMT discussions of all kinds. If you are not sure you have= found a bug, discuss it here first. To formally report bugs or request features, please register and add New Iss= ue on <a href=3D"http://gmt.soest.hawaii.edu">gmt.soest.hawaii.edu</a> To unsubscribe, send the message "signoff gmt-help" to <a href=3D"mailto:lis= [email protected]">[email protected]</a> Note: gmt-help will become obsolete on Sept 1, 2014 - please use forum on <a= href=3D"http://gmt.soest.hawaii.edu">gmt.soest.hawaii.edu</a> instead. </div></blockquote></body></html>= Mailing list for GMT discussions of all kinds. If you are not sure you have found a bug, discuss it here first. To formally report bugs or request features, please register and add New Issue on gmt.soest.hawaii.edu To unsubscribe, send the message "signoff gmt-help" to <a href=3D"mailto:[email protected]">[email protected]</a> Note: gmt-help will become obsolete on Sept 1, 2014 - please use forum on gmt.soest.hawaii.edu instead. --Apple-Mail-5E45EBD2-475B-43A9-9F72-A9B6731F5073--