Leslie: Great, glad to hear it! Regards,
Doug [email protected] Software Engineer UCAR - COSMIC, Tel. (303) 497-2611 On Thu, 24 Sep 2009, Leslie(Pete) Boyd wrote: > > Hi Doug, > > THANKS!!! > > ./configure FC=pgf90 CPPFLAGS="-DNDEBUG -DpgiFortran -fPIC" > > That FIXED it! > > Have a nice day! > > >> Date: Wed, 23 Sep 2009 15:32:02 -0600 (MDT) >> From: Doug Hunt <[email protected]> >> X-X-Sender: [email protected] >> To: "Leslie(Pete) Boyd" <[email protected]> >> cc: [email protected] >> Subject: Re: Assistance with PDL::NetCDF >> User-Agent: Alpine 1.10 (LRH 962 2008-03-14) >> MIME-Version: 1.0 >> X-PMX-Version: 5.4.2.338381, Antispam-Engine: 2.6.0.325393, Antispam-Data: > 2009.9.23.212418 >> X-PerlMx-Spam: Gauge=X, Probability=10%, Report='LINES_OF_YELLING_3 0.671, > BODY_SIZE_10000_PLUS 0, FROM_EDU_TLD 0, __BOUNCE_CHALLENGE_SUBJ 0, > __C230066_P5 > 0, __CP_URI_IN_BODY 0, __CT 0, __CT_TEXT_PLAIN 0, __HAS_MSGID 0, > __LINES_OF_YELLING 0, __MIME_TEXT_ONLY 0, __MIME_VERSION 0, __RUS_OBFU_PHONE > 0, > __SANE_MSGID 0, __TO_MALFORMED_2 0, __USER_AGENT 0' >> >> Hi Leslie: I just noticed these lines: >> >> /usr/bin/ld: /usr/local/lib/libnetcdf.a(attr.o): relocation R_X86_64_32 > against >> `a local symbol' can not be used when making a shared object; recompile >> with -fPIC >> /usr/local/lib/libnetcdf.a: could not read symbols: Bad value >> >> Is your netcdf library compiled with -fPIC? When I compile mine >> on an x86_64 linux system, I do something like: >> >> ./configure FC=pgf90 CPPFLAGS="-DNDEBUG -DpgiFortran -fPIC" > FFLAGS="-I/usr/include" >> >> (note the -fPIC) >> >> Just a thought... >> >> --Doug >> >> >> [email protected] >> Software Engineer >> UCAR - COSMIC, Tel. (303) 497-2611 >> >> On Wed, 23 Sep 2009, Leslie(Pete) Boyd wrote: >> >>> >>> Hi Doug, >>> >>> Thanks for the response and your assistance with this problem. >>> >>> The output below is an attempt to install PDL::NetCDF-4.02 on >>> yet another 64bit server. >>> >>> The OS is: >>> [r...@global6 tmp]# more /etc/*release >>> CentOS release 5.3 (Final) >>> [r...@global6 tmp]# >>> >>> and it is patched to current. >>> >>> I am using CPANPLUS as CPAN cannot find PDL::NetCDF. >>> >>> I have also downloaded PDL-NetCDF-4.02 and attempted to >>> install with "perl Makefile.PL" with identical failures. >>> >>> I am not getting much help from Google. >>> >>> FYI: I installed NetCDF in /usr/local from source. >>> >>> Any suggestions? >>> >>> Thanks. >>> >>> >>> [r...@global6 CPANPLUS-0.88]# cpanp -i >>> http://search.cpan.org/CPAN/authors/id/D/DH/DHUNT/PDL-NetCDF-4.02.tar.gz >>> Installing PDL::NetCDF (4.02) >>> Running [/usr/bin/perl /usr/bin/cpanp-run-perl >>> /root/.cpanplus/5.8.8/build/PDL-NetCDF-4.02/Makefile.PL]... >>> Found libnetcdf.a at /usr/local/lib/libnetcdf.a >>> Found netcdf.h at /usr/local/include/netcdf.h >>> Defining bool=int (linux seems to need this) >>> Writing Makefile for PDL::NetCDF >>> [ERROR] This distribution depends on PDL, but the latest version of PDL on > CPAN >>> (2.004004) doesn't satisfy the specific version dependency (2.2). You may > have >>> to resolve this dependency manually. >>> >>> [ERROR] This distribution depends on PDL, but the latest version of PDL on > CPAN >>> (2.004004) doesn't satisfy the specific version dependency (2.2). You may > have >>> to resolve this dependency manually. >>> >>> >>> Module 'PDL::NetCDF' requires 'PDL' to be installed >>> >>> If you don't wish to see this question anymore >>> you can disable it by entering the following commands on the prompt: >>> 's conf prereqs 1; s save' >>> >>> >>> 1> Yes >>> 2> No >>> 3> Yes to all (for this module) >>> 4> No to all (for this module) >>> >>> >>> Should I install this > module? >>> [1]: >>> [ERROR] MAKE failed: Bad file descriptor Skip blib/lib/PDL/NetCDF.pm > (unchanged) >>> gcc -c > -I/usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/PDL/Core >>> -I/usr/local/include -Dbool=int -g -O2 -g -pipe -Wall > -Wp,-D_FORTIFY_SOURCE=2 >>> -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic >>> -DVERSION=\"4.02\" -DXS_VERSION=\"4.02\" -fPIC >>> "-I/usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/CORE" NetCDF.c >>> In file included from >>> /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/CORE/perl.h:2120, >>> from NetCDF.xs:6: >>> /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/CORE/handy.h:85:1: warning: >>> "bool" redefined >>> <command line>:1:1: warning: this is the location of the previous definition >>> NetCDF.xs: In function ?XS_PDL__NetCDF_nc_put_att_schar?: >>> NetCDF.xs:668: warning: pointer targets in passing argument 6 of >>> ?nc_put_att_schar? differ in signedness >>> NetCDF.xs: In function ?XS_PDL__NetCDF_nc_get_att_schar?: >>> NetCDF.xs:686: warning: pointer targets in passing argument 4 of >>> ?nc_get_att_schar? differ in signedness >>> NetCDF.xs: In function ?XS_PDL__NetCDF_nc_put_vara_schar?: >>> NetCDF.xs:1178: warning: pointer targets in passing argument 5 of >>> ?nc_put_vara_schar? differ in signedness >>> NetCDF.xs: In function ?XS_PDL__NetCDF_nc_get_vara_schar?: >>> NetCDF.xs:1200: warning: pointer targets in passing argument 5 of >>> ?nc_get_vara_schar? differ in signedness >>> NetCDF.xs: In function ?XS_PDL__NetCDF_nc_put_var_schar?: >>> NetCDF.xs:1510: warning: pointer targets in passing argument 3 of >>> ?nc_put_var_schar? differ in signedness >>> NetCDF.xs: In function ?XS_PDL__NetCDF_nc_get_var_schar?: >>> NetCDF.xs:1527: warning: pointer targets in passing argument 3 of >>> ?nc_get_var_schar? differ in signedness >>> Running Mkbootstrap for PDL::NetCDF () >>> chmod 644 NetCDF.bs >>> rm -f blib/arch/auto/PDL/NetCDF/NetCDF.so >>> gcc -shared -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions >>> -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic NetCDF.o > -o >>> blib/arch/auto/PDL/NetCDF/NetCDF.so \ >>> -L/usr/local/lib -lnetcdf \ >>> >>> /usr/bin/ld: /usr/local/lib/libnetcdf.a(attr.o): relocation R_X86_64_32 > against >>> `a local symbol' can not be used when making a shared object; recompile with >>> -fPIC >>> /usr/local/lib/libnetcdf.a: could not read symbols: Bad value >>> collect2: ld returned 1 exit status >>> make: *** [blib/arch/auto/PDL/NetCDF/NetCDF.so] Error 1 >>> >>> >>> [ERROR] Unable to create a new distribution object for 'PDL::NetCDF' -- > cannot >>> continue >>> >>> *** Install log written to: >>> /root/.cpanplus/install-logs/PDL-NetCDF-4.02-1253728838.log >>> >>> Error installing 'PDL::NetCDF' >>> Problem installing one or more modules >>> >>> [r...@global6 CPANPLUS-0.88]# >>> >>>> Date: Tue, 22 Sep 2009 16:41:07 -0600 (MDT) >>>> From: Doug Hunt <[email protected]> >>>> X-X-Sender: [email protected] >>>> To: "Leslie(Pete) Boyd" <[email protected]> >>>> cc: [email protected] >>>> Subject: Re: Assistance with PDL::NetCDF >>>> User-Agent: Alpine 1.10 (LRH 962 2008-03-14) >>>> MIME-Version: 1.0 >>>> X-PMX-Version: 5.4.2.338381, Antispam-Engine: 2.6.0.325393, Antispam-Data: >>> 2009.9.22.223055 >>>> X-PerlMx-Spam: Gauge=X, Probability=10%, Report='LINES_OF_YELLING_3 0.671, >>> FROM_EDU_TLD 0, __BOUNCE_CHALLENGE_SUBJ 0, __C230066_P5 0, __CP_URI_IN_BODY > 0, >>> __CT 0, __CT_TEXT_PLAIN 0, __HAS_MSGID 0, __LINES_OF_YELLING 0, > __MIME_TEXT_ONLY >>> 0, __MIME_VERSION 0, __RUS_OBFU_PHONE 0, __SANE_MSGID 0, __TO_MALFORMED_2 0, >>> __USER_AGENT 0' >>>> >>>> Leslie: x86_64 architecture I'm quite familiar with. But the errors you >>>> sent in your last email seemed to come from a perl installed on an ia64 >>>> machine. >>>> >>>> --Doug >>>> >>>> [email protected] >>>> Software Engineer >>>> UCAR - COSMIC, Tel. (303) 497-2611 >>>> >>>> On Tue, 22 Sep 2009, Leslie(Pete) Boyd wrote: >>>> >>>>> >>>>> Hi Doug, >>>>> >>>>> If it makes a difference, this is x64 architecture. >>>>> >>>>> Thanks for your assistance. >>>>> >>>>>> Date: Tue, 22 Sep 2009 13:46:13 -0600 (MDT) >>>>>> From: Doug Hunt <[email protected]> >>>>>> X-X-Sender: [email protected] >>>>>> To: "Leslie(Pete) Boyd" <[email protected]> >>>>>> cc: [email protected], [email protected] >>>>>> Subject: Re: Assistance with PDL::NetCDF >>>>>> User-Agent: Alpine 1.10 (LRH 962 2008-03-14) >>>>>> MIME-Version: 1.0 >>>>>> X-PMX-Version: 5.4.2.338381, Antispam-Engine: 2.6.0.325393, > Antispam-Data: >>>>> 2009.9.22.193617 >>>>>> X-PerlMx-Spam: Gauge=IIIIIII, Probability=7%, Report='BODY_SIZE_5000_5999 >>> 0, >>>>> BODY_SIZE_7000_LESS 0, FROM_EDU_TLD 0, __BOUNCE_CHALLENGE_SUBJ 0, >>> __C230066_P5 >>>>> 0, __CP_URI_IN_BODY 0, __CT 0, __CT_TEXT_PLAIN 0, __HAS_MSGID 0, >>>>> __MIME_TEXT_ONLY 0, __MIME_VERSION 0, __RUS_OBFU_PHONE 0, __SANE_MSGID 0, >>>>> __TO_MALFORMED_2 0, __USER_AGENT 0' >>>>>> >>>>>> Hi Leslie: I'm not familiar with the tool you are using 'cpanp'. >>>>>> >>>>>> If you've got PDL 2.4.4_08 installed under the same library directory as >>>>>> perl on your system, you should be able to just install PDL-NetCDF by: >>>>>> >>>>>> 1) tar -xvf PDL-NetCDF.version.tar.gz >>>>>> 2) cd PDL-NetCDF.version >>>>>> 3) export NETCDF_LIBDIR=/usr/local/lib >>>>>> 4) export NETCDF_INCDIR=/usr/local/include >>>>>> >>>>>> # Make sure this is the same perl as you installed PDL under! >>>>>> 5) perl Makefile.PL >>>>>> 6) make >>>>>> 7) make test >>>>>> 8) make install >>>>>> >>>>>> Please try this and send me output from whatever stage fails. >>>>>> >>>>>> Regards, >>>>>> >>>>>> Doug Hunt >>>>>> >>>>>> [email protected] >>>>>> Software Engineer >>>>>> UCAR - COSMIC, Tel. (303) 497-2611 >>>>>> >>>>>> On Tue, 22 Sep 2009, Leslie(Pete) Boyd wrote: >>>>>> >>>>>>> >>>>>>> Hi Dan, >>>>>>> >>>>>>> I'm in trouble again. >>>>>>> >>>>>>> Could you give me some advice on this error. >>>>>>> >>>>>>> I do have PDL-2.4.4_08 installed: >>>>>>> hail:/tmp/PDL # perl -MPDL -e 'print "$PDL::VERSION\n"' >>>>>>> 2.4.4_08 >>>>>>> >>>>>>> Thanks. >>>>>>> >>>>>>> hail:~ # cpanp -i >>>>>>> http://search.cpan.org/CPAN/authors/id/D/DH/DHUNT/PDL-NetCDF-4.02.tar.gz >>>>>>> Installing PDL::NetCDF (4.02) >>>>>>> Running [/usr/bin/perl /usr/bin/cpanp-run-perl >>>>>>> /root/.cpanplus/5.8.8/build/PDL-NetCDF-4.02/Makefile.PL]... >>>>>>> Found libnetcdf.a at /usr/local/lib/libnetcdf.a >>>>>>> Found netcdf.h at /usr/local/include/netcdf.h >>>>>>> Defining bool=int (linux seems to need this) >>>>>>> Writing Makefile for PDL::NetCDF >>>>>>> [ERROR] This distribution depends on PDL, but the latest version of PDL > on >>>>> CPAN >>>>>>> (2.004004) doesn't satisfy the specific version dependency (2.2). You > may >>>>> have >>>>>>> to resolve this dependency manually. >>>>>>> >>>>>>> [ERROR] This distribution depends on PDL, but the latest version of PDL > on >>>>> CPAN >>>>>>> (2.004004) doesn't satisfy the specific version dependency (2.2). You > may >>>>> have >>>>>>> to resolve this dependency manually. >>>>>>> >>>>>>> >>>>>>> Module 'PDL::NetCDF' requires 'PDL' to be installed >>>>>>> >>>>>>> If you don't wish to see this question anymore >>>>>>> you can disable it by entering the following commands on the prompt: >>>>>>> 's conf prereqs 1; s save' >>>>>>> >>>>>>> >>>>>>> 1> Yes >>>>>>> 2> No >>>>>>> 3> Yes to all (for this module) >>>>>>> 4> No to all (for this module) >>>>>>> >>>>>>> Should I install this module? [1]: >>>>>>> [ERROR] MAKE failed: Bad file descriptor cc -c >>>>>>> -I/usr/lib/perl5/site_perl/5.8.8/ia64-linux-thread-multi/PDL/Core >>>>>>> -I/usr/local/include -Dbool=int -g -O2 -fmessage-length=0 -Wall >>>>>>> -D_FORTIFY_SOURCE=2 -g -Wall -pipe -DVERSION=\"4.02\" >>>>> -DXS_VERSION=\"4.02\" >>>>>>> -fPIC "-I/usr/lib/perl5/5.8.8/ia64-linux-thread-multi/CORE" NetCDF.c >>>>>>> In file included from >>>>>>> /usr/lib/perl5/5.8.8/ia64-linux-thread-multi/CORE/perl.h:2120, >>>>>>> from NetCDF.xs:6: >>>>>>> /usr/lib/perl5/5.8.8/ia64-linux-thread-multi/CORE/handy.h:85:1: warning: >>>>> "bool" >>>>>>> redefined >>>>>>> <command line>:1:1: warning: this is the location of the previous >>> definition >>>>>>> NetCDF.xs: In function ?XS_PDL__NetCDF_nc_put_att_schar?: >>>>>>> NetCDF.xs:668: warning: pointer targets in passing argument 6 of >>>>>>> ?nc_put_att_schar? differ in signedness >>>>>>> NetCDF.xs: In function ?XS_PDL__NetCDF_nc_get_att_schar?: >>>>>>> NetCDF.xs:686: warning: pointer targets in passing argument 4 of >>>>>>> ?nc_get_att_schar? differ in signedness >>>>>>> NetCDF.xs: In function ?XS_PDL__NetCDF_nc_put_vara_schar?: >>>>>>> NetCDF.xs:1178: warning: pointer targets in passing argument 5 of >>>>>>> ?nc_put_vara_schar? differ in signedness >>>>>>> NetCDF.xs: In function ?XS_PDL__NetCDF_nc_get_vara_schar?: >>>>>>> NetCDF.xs:1200: warning: pointer targets in passing argument 5 of >>>>>>> ?nc_get_vara_schar? differ in signedness >>>>>>> NetCDF.xs: In function ?XS_PDL__NetCDF_nc_put_var_schar?: >>>>>>> NetCDF.xs:1510: warning: pointer targets in passing argument 3 of >>>>>>> ?nc_put_var_schar? differ in signedness >>>>>>> NetCDF.xs: In function ?XS_PDL__NetCDF_nc_get_var_schar?: >>>>>>> NetCDF.xs:1527: warning: pointer targets in passing argument 3 of >>>>>>> ?nc_get_var_schar? differ in signedness >>>>>>> Running Mkbootstrap for PDL::NetCDF () >>>>>>> chmod 644 NetCDF.bs >>>>>>> rm -f blib/arch/auto/PDL/NetCDF/NetCDF.so >>>>>>> cc -shared NetCDF.o -o blib/arch/auto/PDL/NetCDF/NetCDF.so \ >>>>>>> -L/usr/local/lib -lnetcdf \ >>>>>>> >>>>>>> /usr/lib/gcc/ia64-suse-linux/4.1.2/../../../../ia64-suse-linux/bin/ld: >>>>>>> /usr/local/lib/libnetcdf.a(nc.o): @gprel relocation against dynamic > symbol >>>>>>> default_create_format >>>>>>> /usr/lib/gcc/ia64-suse-linux/4.1.2/../../../../ia64-suse-linux/bin/ld: >>>>>>> /usr/local/lib/libnetcdf.a(nc.o): @gprel relocation against dynamic > symbol >>>>>>> default_create_format >>>>>>> /usr/lib/gcc/ia64-suse-linux/4.1.2/../../../../ia64-suse-linux/bin/ld: >>>>>>> /usr/local/lib/libnetcdf.a(nc.o): @gprel relocation against dynamic > symbol >>>>>>> default_create_format >>>>>>> /usr/lib/gcc/ia64-suse-linux/4.1.2/../../../../ia64-suse-linux/bin/ld: >>> final >>>>>>> link failed: Nonrepresentable section on output >>>>>>> collect2: ld returned 1 exit status >>>>>>> make: *** [blib/arch/auto/PDL/NetCDF/NetCDF.so] Error 1 >>>>>>> >>>>>>> >>>>>>> [ERROR] Unable to create a new distribution object for 'PDL::NetCDF' -- >>>>> cannot >>>>>>> continue >>>>>>> >>>>>>> *** Install log written to: >>>>>>> /root/.cpanplus/install-logs/PDL-NetCDF-4.02-1253644469.log >>>>>>> >>>>>>> Error installing 'PDL::NetCDF' >>>>>>> Problem installing one or more modules >>>>>>> >>>>>>> hail:~ # >>>>>>> >>>>>>> ****************** >>>>>>> Leslie(Pete) Boyd >>>>>>> Contractor: The rich man isn't the one who has the most, >>>>>>> Vision Technoligies but the one who needs the least. >>>>>>> Senior Systems Engineer >>>>>>> US EPA Rm. E460 --- IN GOD WE TRUST -- >>>>>>> 919/541-1438 >>>>>>> ****************** >>>>>>> >>>>>>> >>>>>>> >>>>> >>>>> ****************** >>>>> Leslie(Pete) Boyd >>>>> Contractor: The rich man isn't the one who has the most, >>>>> Vision Technoligies but the one who needs the least. >>>>> Senior Systems Engineer >>>>> US EPA Rm. E460 --- IN GOD WE TRUST -- >>>>> 919/541-1438 >>>>> ****************** >>>>> >>>>> >>> >>> ****************** >>> Leslie(Pete) Boyd >>> Contractor: The rich man isn't the one who has the most, >>> Vision Technoligies but the one who needs the least. >>> Senior Systems Engineer >>> US EPA Rm. E460 --- IN GOD WE TRUST -- >>> 919/541-1438 >>> ****************** >>> >>> >>> > > ****************** > Leslie(Pete) Boyd > Contractor: The rich man isn't the one who has the most, > Vision Technoligies but the one who needs the least. > Senior Systems Engineer > US EPA Rm. E460 --- IN GOD WE TRUST -- > 919/541-1438 > ****************** > > _______________________________________________ Perldl mailing list [email protected] http://mailman.jach.hawaii.edu/mailman/listinfo/perldl
