Re: Fw: HDF5 error with gmt 4.5.12
Paul Wessel <[email protected]> Fri, 15 Aug 2014 08:25:03 -1000
| Newsgroups | gmane.comp.gis.gmt.user |
|---|---|
| Message-ID | <[email protected]> |
--Apple-Mail=_8DBE1A61-2DF8-4800-98E7-40BF9B8B5BC1 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=utf-8 Hi Gery- While I had to suffer through the indignity of running GMT 5 under = Cygwin for a class, I did so without gdal since there was no gdal cygwin = package 6 months ago. Are you saying there now is a gdal package via = setup.exe? The GMT cygwin install instructions on the GMT wiki are the = instructions I wrote after installing it myself so they work as recently = as March. You must have a good reason not to dual-boot your machine into ubuntu = since you are willing to put up with cygwin. -p On Aug 15, 2014, at 7:32 AM, Gery . <[email protected]> wrote: > Even though I use > export HDF5_DISABLE_VERSION_CHECK=3D1 > export HDF5_DISABLE_VERSION_CHECK=3D2 > I am wondering if Cygwin can be eventually unstable? or even my pc = explode? 8-) >=20 > Thanks for any pointers >=20 > Sent from Windows Mail >=20 > From: Gery . > Sent: =E2=80=8EFriday=E2=80=8E, =E2=80=8EAugust=E2=80=8E =E2=80=8E15=E2=80= =8E, =E2=80=8E2014 =E2=80=8E7=E2=80=8E:=E2=80=8E05=E2=80=8E =E2=80=8EPM > To: World-Wide GMT Usage and Help Mailing List >=20 > Sorry for the last noisy message, but things were smooth finally, the = solution was to install without gdal. Now things work, but I received = this message 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 = continues. >=20 > This can happen when an application was compiled by one version of = HDF5 but >=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) = 2014-05-23 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 = -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 >=20 > H5_CFLAGS: -std=3Dc99 -pedantic -Wall -Wextra -Wundef -Wshadow = -Wpointer-arith -Wbad-function-cast -Wcast-qual -Wcast-align = -Wwrite-strings -Wconversion -Waggregate-return -Wstrict-prototypes = -Wmissing-prototypes -Wmissing-declarations -Wre dundant-decls = -Wnested-externs -Winline -Wfloat-equal -Wmissing-format-attribute = -Wmissing-noreturn -Wpacked -Wdisabled-optimizati on -Wformat=3D2 = -Wunreachable-code -Wendif-labels -Wdeclaration-after-statement = -Wold-style-definition -Winvalid-pch -Wvariadic-macr os -Winit-self = -Wmissing-include-dirs -Wswitch-default -Wswitch-enum -Wunused-macros = -Wunsafe-loop-optimizations -Wc++-compat -Wst rict-overflow -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 = -Wvector-operation-performance -Wsuggest-attribute=3Dpure = -Wsuggest-attribute=3Dnoreturn -Wsuggest-attribute=3Dformat -O3 = -fomit-frame- pointer -finline-functions >=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/hdf5-1.8.13-1/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 >=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? this 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 = 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. 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=_8DBE1A61-2DF8-4800-98E7-40BF9B8B5BC1 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=utf-8 <html><head><meta http-equiv=3D"Content-Type" content=3D"text/html = charset=3Dutf-8"></head><body style=3D"word-wrap: break-word; = -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;">Hi = Gery-<div><br></div><div>While I had to suffer through the indignity of = running GMT 5 under Cygwin for a class, I did so without gdal since = there was no gdal cygwin package 6 months ago. Are you saying there now = is a gdal package via setup.exe? The GMT cygwin install = instructions on the GMT wiki are the instructions I wrote after = installing it myself so they work as recently as = March.</div><div><div><br><div>You must have a good reason not to = dual-boot your machine into ubuntu since you are willing to put up with = cygwin.</div><div><br><div>-p</div><div><br><div><div>On Aug 15, 2014, = at 7:32 AM, Gery . <<a = href=3D"mailto:[email protected]">[email protected]</a>> = wrote:</div><br class=3D"Apple-interchange-newline"><blockquote = type=3D"cite"> <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.MsoListParagraphCxSpFirst,=20 p.MsoListParagraphCxSpMiddle, li.MsoListParagraphCxSpMiddle, = div.MsoListParagraphCxSpMiddle,=20 p.MsoListParagraphCxSpLast, li.MsoListParagraphCxSpLast, = div.MsoListParagraphCxSpLast { margin-top:0in; margin-right:0in; margin-bottom:0in; margin-left:.5in; margin-bottom:.0001pt; line-height:115%; } --></style> <div dir=3D"ltr"> <div data-externalstyle=3D"false" dir=3D"ltr" style=3D"font-family: = 'Calibri', 'Segoe UI', 'Meiryo', 'Microsoft YaHei UI', 'Microsoft = JhengHei UI', 'Malgun Gothic', 'sans-serif';font-size:12pt;"><div>Even = though I use </div><div><pre style=3D"text-transform: none; line-height: = normal; text-indent: 0px; letter-spacing: normal; padding-left: 0.7em; = font-size: 12px; font-style: normal; font-variant: normal; font-weight: = normal; word-spacing: 0px; white-space: pre-wrap; max-width: 80em; = background-color: rgb(255, 255, 255); -webkit-text-stroke-width: = 0px;">export HDF5_DISABLE_VERSION_CHECK=3D1</pre></div><div><pre = style=3D"text-transform: none; line-height: normal; text-indent: 0px; = letter-spacing: normal; padding-left: 0.7em; font-size: 12px; = font-style: normal; font-variant: normal; font-weight: normal; = word-spacing: 0px; white-space: pre-wrap; max-width: 80em; = background-color: rgb(255, 255, 255); -webkit-text-stroke-width: = 0px;">export HDF5_DISABLE_VERSION_CHECK=3D2</pre></div><div>I am = wondering if Cygwin can be eventually unstable? or even my pc explode? = 8-)</div><div><br></div><div>Thanks for any pointers<br></div><div = data-signatureblock=3D"true"><div><br></div><div>Sent from Windows = Mail</div><div><br></div></div><div style=3D"padding-top: 5px; = border-top-color: rgb(229, 229, 229); border-top-width: 1px; = border-top-style: solid;"><font face=3D" 'Calibri', 'Segoe UI', = 'Meiryo', 'Microsoft YaHei UI', 'Microsoft JhengHei UI', 'Malgun = Gothic', 'sans-serif'" style=3D"line-height: 15pt; letter-spacing: = 0.02em; font-family: "Calibri", "Segoe UI", = "Meiryo", "Microsoft YaHei UI", "Microsoft = JhengHei UI", "Malgun Gothic", "sans-serif"; = font-size: 12pt;"><b>From:</b> <a = href=3D"mailto:[email protected]" target=3D"_parent">Gery = .</a><br><b>Sent:</b> =E2=80=8EFriday=E2=80=8E, =E2=80=8EAugust=E2=80= =8E =E2=80=8E15=E2=80=8E, =E2=80=8E2014 =E2=80=8E7=E2=80=8E:=E2=80=8E05=E2= =80=8E =E2=80=8EPM<br><b>To:</b> <a = href=3D"mailto:[email protected]" target=3D"_parent">World-Wide = GMT Usage and Help Mailing List</a></font></div><div><br></div><div = dir=3D"ltr"> <div>Sorry for the last noisy message, but things were smooth finally, = the solution was to install without gdal. 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 -Ia -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 continues.</p><p>This can happen = when an application was compiled by one version of HDF5 but</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 environment</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-declaration = -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 -Wundef -Wshadow -Wpointer-arith = -Wbad-function-cast -Wcast-qual -Wcast-align = -Wwrite-strings -Wconversion -Waggregate-return -Wstrict-prototypes = -Wmissing-prototypes -Wmissing-declarations -Wre = dundant-decls -Wnested-externs -Winline -Wfloat-equal = -Wmissing-format-attribute -Wmissing-noreturn -Wpacked = -Wdisabled-optimizati on -Wformat=3D2 = -Wunreachable-code -Wendif-labels -Wdeclaration-after-statement = -Wold-style-definition -Winvalid-pch -Wvariadic-macr = os -Winit-self -Wmissing-include-dirs -Wswitch-default -Wswitch-enum = -Wunused-macros -Wunsafe-loop-optimizations -Wc++-compat -Wst = rict-overflow -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 -Wvector-operation-performance = -Wsuggest-attribute=3Dpure -Wsuggest-attribute=3Dnoreturn = -Wsuggest-attribute=3Dformat -O3 -fomit-frame- pointer = -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/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 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 HDF5 = 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></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 = Issue 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:[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. </blockquote></div><br></div></div></div></div></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=_8DBE1A61-2DF8-4800-98E7-40BF9B8B5BC1--