Re: ncl - libbz2 shared libraries

Mack,

It seems that a number of system libraries are installed incorrectly on your system. As with the libbz2 library, you can try googling the error, as there's usually several references to a solution.

On our Linux system, libcurl-gnutls.so.4.2.0 is linked to libcurl.a:

lrwxrwxrwx 1 root root 16 Nov 26 10:26 /usr/lib/libcurl.a -> libcurl-gnutls.a
-rw-r--r-- 1 root root 432996 Nov 19 16:01 /usr/lib/libcurl-gnutls.a
-rw-r--r-- 1 root root 979 Nov 19 16:01 /usr/lib/libcurl-gnutls.la
lrwxrwxrwx 1 root root 23 Nov 26 10:26 /usr/lib/libcurl-gnutls.so -> libcurl-gnutls.so.4.2.0
lrwxrwxrwx 1 root root 19 Nov 26 10:26 /usr/lib/libcurl-gnutls.so.3 -> libcurl-gnutls.so.4
lrwxrwxrwx 1 root root 23 Nov 26 10:26 /usr/lib/libcurl-gnutls.so.4 -> libcurl-gnutls.so.4.2.0
-rw-r--r-- 1 root root 320056 Nov 19 16:01 /usr/lib/libcurl-gnutls.so.4.2.0

You need to make sure you have libcurl installed on your system, and that it was installed correctly.

--Mary

On Feb 3, 2014, at 1:13 PM, Mack J. Jenkins <mack.jenkins@eas.gatech.edu> wrote:

> Actually, that worked, but now it has generated a new issue. I think this one is just I need to find the correct package for libcurl-gnutls.
>
> ncl: error while loading shared libraries: libcurl-gnutls.so.4: cannot open shared object file: No such file or directory
>
> And if I try creating a sym link to the
>
> /usr/lib/libcurl-gnutls.so.4
>
> It complains that it is the 32bit version. But this is at least progress.
>
> --
> Mack J. Jenkins, II
> 404-385-1591
> mack.jenkins@eas.gatech.edu
> System Support Engineer II
> Earth & Atmospheric Sciences
>
> From: "Mary Haley" <haley@ucar.edu>
> To: "Mack J. Jenkins" <mack.jenkins@eas.gatech.edu>
> Cc: "ncl-install@ucar.edu ncl-install@ucar.edu" <ncl-install@ucar.edu>
> Sent: Friday, January 31, 2014 2:04:18 PM
> Subject: Re: ncl - libbz2 shared libraries
>
> Mack,
>
> The issue appears to be that you don’t have the file “/lib64/libbz2.so.1.0”.
>
> You have "/lib64/libbz2.so.1.0.6” and "/lib64/libbz2.so.1”, but NCL wants "/lib64/libbz2.so.1.0”.
>
> I looked on various LINUX systems that we have, and we always have all three files:
>
> lrwxrwxrwx 1 root root 15 Mar 25 2012 /lib64/libbz2.so.1 -> libbz2.so.1.0.6
> lrwxrwxrwx 1 root root 15 Mar 25 2012 /lib64/libbz2.so.1.0 -> libbz2.so.1.0.6
> -rw-r--r-- 1 root root 66944 Dec 26 2011 /lib64/libbz2.so.1.0.6
>
> You should try googling this error message. I found several suggestions, some of which suggested linking the file yourself:
>
> sudo ln -s /lib64/libbz2.so.1.0.6 /lib64/libbz2.so.1.0
>
> This method is not generally recommended, however, because it’s just a hack for what is potentially a broken install of bz2.
> Did you try reinstalling bz2?
>
> —Mary
>
> On Jan 31, 2014, at 9:53 AM, Mack J. Jenkins <mack.jenkins@eas.gatech.edu> wrote:
>
> [root@server]# ls -l /lib/libbz2*
> lrwxrwxrwx 1 root root 15 Feb 21 2012 /lib/libbz2.so.1 -> libbz2.so.1.0.6
> lrwxrwxrwx 1 root root 15 Jan 27 09:46 /lib/libbz2.so.1.0 -> libbz2.so.1.0.6
> lrwxrwxrwx 1 root root 15 Jan 27 09:47 /lib/libbz2.so.1.0.4 -> libbz2.so.1.0.6
> -rwxr-xr-x 1 root root 62056 Oct 29 2011 /lib/libbz2.so.1.0.6
>
>
> [root@server]# ls -l /lib64/libbz2*
> lrwxrwxrwx 1 root root 15 Nov 10 2011 /lib64/libbz2.so.1 -> libbz2.so.1.0.6
> -rwxr-xr-x 1 root root 62848 Oct 29 2011 /lib64/libbz2.so.1.0.6
>
>
> I went and looked, there is a
> /lib64/libbz2.so.1 that points to /lib64/libbz2.so.1.0.6
>
>
> As for how was bzip2 installed, it's a binary that was installed with Yast.
>
>
> --
> Mack J. Jenkins, II
> 404-385-1591
> mack.jenkins@eas.gatech.edu
> System Support Engineer II
> Earth & Atmospheric Sciences
>
> ----- Original Message -----
> From: "Mary Haley" <haley@ucar.edu>
> To: "Mack J. Jenkins" <mack.jenkins@eas.gatech.edu>
> Cc: ncl-install@ucar.edu, "Brandon Fisel" <bjfisel@gmail.com>
> Sent: Tuesday, January 28, 2014 6:33:23 PM
> Subject: Re: ncl - libbz2 shared libraries
>
> 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@eas.gatech.edu> wrote:
>
> I am having this same issue, and after running the ldd I get the following.
>
> [root@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@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@eas.gatech.edu
> System Support Engineer II
> Earth & Atmospheric Sciences
>
> ----- Original Message -----
> From: "Mary Haley" <haley@ucar.edu>
> To: "Brandon Fisel" <bjfisel@gmail.com>
> Cc: ncl-install@ucar.edu
> Sent: Tuesday, October 22, 2013 12:33:30 PM
> Subject: Re: 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@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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Received on Fri Feb 7 16:34:02 2014