[ncl-install] ncl - libbz2 shared libraries
Mary Haley
haley at ucar.edu
Tue Jan 28 16:33:23 MST 2014
It still looks like there's something odd about your bz2 libraries. You have:
> /lib/libbz2.so.1
> /lib/libbz2.so.1.0
> /lib/libbz2.so.1.0.4
> /lib/libbz2.so.1.0.6
> /lib64/libbz2.so.1
> /lib64/libbz2.so.1.0.6
It's a bit suspicious that you have 1.0.6 and 1.0.4 versions.
What does:
ls -l /lib/libbz2*
ls -l /lib64/libbz2*
report?
Also, the fact that there's no "/lib64/libbz2.so.1.0" file is also suspicious.
How was bz2 installed? On two of our Linux systems, it looks like this:
lrwxrwxrwx 1 root root 15 Mar 25 2012 /lib/libbz2.so.1 -> libbz2.so.1.0.4
lrwxrwxrwx 1 root root 15 Mar 25 2012 /lib/libbz2.so.1.0 -> libbz2.so.1.0.4
-rw-r--r-- 1 root root 70428 Dec 26 2011 /lib/libbz2.so.1.0.4
--Mary
On Jan 28, 2014, at 7:46 AM, Mack J. Jenkins <mack.jenkins at eas.gatech.edu> wrote:
> I am having this same issue, and after running the ldd I get the following.
>
> [root at server]# ldd ncl
> ./ncl: /usr/lib64/libcurl-gnutls.so.4: no version information available (required by ./ncl)
> linux-vdso.so.1 => (0x00007fff3f9ed000)
> libcurl-gnutls.so.4 => /usr/lib64/libcurl-gnutls.so.4 (0x00002b6c0e5dc000)
> libpthread.so.0 => /lib64/libpthread.so.0 (0x00002b6c0e83d000)
> libbz2.so.1.0 => not found
> libXrender.so.1 => /usr/lib64/libXrender.so.1 (0x00002b6c0ea5a000)
> libX11.so.6 => /usr/lib64/libX11.so.6 (0x00002b6c0ec66000)
> libXext.so.6 => /usr/lib64/libXext.so.6 (0x00002b6c0efa7000)
> libm.so.6 => /lib64/libm.so.6 (0x00002b6c0f1ba000)
> libdl.so.2 => /lib64/libdl.so.2 (0x00002b6c0f412000)
> libstdc++.so.6 => /usr/lib64/libstdc++.so.6 (0x00002b6c0f616000)
> libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00002b6c0f920000)
> libc.so.6 => /lib64/libc.so.6 (0x00002b6c0fb37000)
> /lib64/ld-linux-x86-64.so.2 (0x00002b6c0e3b9000)
> libcares.so.2 => /usr/lib64/libcares.so.2 (0x00002b6c0fec7000)
> libidn.so.11 => /usr/lib64/libidn.so.11 (0x00002b6c100d7000)
> liblber-2.4.so.2 => /usr/lib64/liblber-2.4.so.2 (0x00002b6c1030b000)
> libldap-2.4.so.2 => /usr/lib64/libldap-2.4.so.2 (0x00002b6c1051a000)
> librt.so.1 => /lib64/librt.so.1 (0x00002b6c10763000)
> libgssapi_krb5.so.2 => /dods/matlib/nclibs/dods-lib-master/libgssapi_krb5.so.2 (0x00002b6c1096c000)
> libssl.so.1.0.0 => /lib64/libssl.so.1.0.0 (0x00002b6c10a85000)
> libcrypto.so.1.0.0 => /lib64/libcrypto.so.1.0.0 (0x00002b6c10ce1000)
> libz.so.1 => /lib64/libz.so.1 (0x00002b6c11093000)
> libssh2.so.1 => /usr/lib64/libssh2.so.1 (0x00002b6c112ab000)
> libxcb.so.1 => /usr/lib64/libxcb.so.1 (0x00002b6c114d3000)
> libresolv.so.2 => /lib64/libresolv.so.2 (0x00002b6c116f1000)
> libsasl2.so.2 => /usr/lib64/libsasl2.so.2 (0x00002b6c11908000)
> libkrb5.so.3 => /dods/matlib/nclibs/dods-lib-master/libkrb5.so.3 (0x00002b6c11b24000)
> libk5crypto.so.3 => /dods/matlib/nclibs/dods-lib-master/libk5crypto.so.3 (0x00002b6c11c9f000)
> libcom_err.so.3 => /dods/matlib/nclibs/dods-lib-master/libcom_err.so.3 (0x00002b6c11dc4000)
> libkrb5support.so.0 => /dods/matlib/nclibs/dods-lib-master/libkrb5support.so.0 (0x00002b6c11ec9000)
> libXau.so.6 => /usr/lib64/libXau.so.6 (0x00002b6c11fcc000)
>
> And after a locate libbz2, I get the following,
>
> [root at server]# locate libbz2
> /lib/libbz2.so.1
> /lib/libbz2.so.1.0
> /lib/libbz2.so.1.0.4
> /lib/libbz2.so.1.0.6
> /lib64/libbz2.so.1
> /lib64/libbz2.so.1.0.6
> /root/EAS/libbz2-devel-1.0.6-14.1.4.i586.rpm
> /root/EAS/libbz2-devel-1.0.6-14.1.4.x86_64.rpm
> /usr/lib64/libbz2.so
> /usr/lib64/kde4/kerfuffle_libbz2.so
> /usr/share/doc/packages/libbz2-1
> /usr/share/doc/packages/libbz2-1/COPYING
> /usr/share/doc/packages/libbz2-1/NEWS
> /usr/share/doc/packages/libbz2-1/README
> /usr/share/kde4/services/kerfuffle_libbz2.desktop
>
> I tried
>
> setenv LD_LIBRARY_PATH $HOME:${LD_LIBRARY_PATH}
>
> But that did not get me anywhere. I hope that you can point me in the right direction on this one. AS for which I downloaded, I downloaded the pre-compiled 6.1.2 binary with OPeNDAP-enabled.
> --
> Mack J. Jenkins, II
> 404-385-1591
> mack.jenkins at eas.gatech.edu
> System Support Engineer II
> Earth & Atmospheric Sciences
>
> ----- Original Message -----
> From: "Mary Haley" <haley at ucar.edu>
> To: "Brandon Fisel" <bjfisel at gmail.com>
> Cc: ncl-install at ucar.edu
> Sent: Tuesday, October 22, 2013 12:33:30 PM
> Subject: Re: [ncl-install] ncl - libbz2 shared libraries
>
> Hi Brandon,
>
> I'm not sure if the issue is with a poorly-linked libbz file, or if you have a version of bz2 that is incompatible with what NCL was compiled with.
>
> You didn't quite set the LD_LIBRARY_PATH correctly, as you don't want to include the actual file name in the list.
>
> Try:
>
> setenv LD_LIBRARY_PATH $HOME:${LD_LIBRARY_PATH}
>
> Note that it is generally not recommended to fix shared library issues in this fashion. The true fix is to try to figure out why your system bz2 is not compatible with the one NCL is built with.
>
> Which NCL binary did you download, and what does the following report:
>
> ldd $NCARG_ROOT/bin/ncl
> locate libbz2
>
> --Mary
>
>
> On Oct 21, 2013, at 3:00 PM, Brandon Fisel <bjfisel at gmail.com> wrote:
>
>> Hi,
>>
>> I have downloaded and extracted the ncl v.6.1.2 (nodap) binary and upon running the executable, I am receiving the following:
>> bin/ncl: error while loading shared libraries: libbz2.so.1.0: cannot open shared object file: No such file or directory
>>
>> The system I am using has libbz2.so located in /lib64:
>> libbz2.so.1 libbz2.so.1.0.5
>>
>> I attempted to create a symbolic link to the libbz2.so.1 in my $HOME directory and added the location of the libbz2 to my LD_LIBRARY_PATH, and received the same error as above:
>> ln -s /lib64/libbz2.so.1 $HOME/libbz2.so.1.0
>> setenv LD_LIBRARY_PATH $HOME/libbz2.so.1.0:${LD_LIBRARY_PATH}
>>
>> Following from some previous ncl-install archived discussions, I successfully downloaded and compiled (static and shared) bzip2 libraries, and added the location of the shared library to the LD_LIBRARY_PATH and am still receiving the same error as above.
>>
>> Should I compile the source code rather than use the binaries provided to me?
>>
>> Cheers,
>> -------------------------------------------------------------
>> Brandon J Fisel
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