Re: GCC error and libmpfr.so.4 not found

[Asma Riyaz <asmariyaz23@xxxxxxxxx>]

Hi Jimmy,

I checked linkage with ldd:

ldd /path/to/cc1

Here is the result:

linux-vdso.so.1 =>  (0x00007fffed53f000)

libmpfr.so.4 => /../software/free/Linux/redhat_6_x86_64/pkgs/gcc_4.9.0/lib/libmpfr.so.4 (0x00007f264f304000)

libgmp.so.10 => /../software/free/Linux/redhat_6_x86_64/pkgs/gcc_4.9.0/lib/libgmp.so.10 (0x00007f264f08f000)

libdl.so.2 => /lib64/libdl.so.2 (0x00000034a2800000)

libm.so.6 => /lib64/libm.so.6 (0x00000034a2000000)

libc.so.6 => /lib64/libc.so.6 (0x00000034a1c00000)

/lib64/ld-linux-x86-64.so.2 (0x00000034a1800000)

libmpfr.so.4 already exists but it still didn't find it.

I will now export LD_LIBRARY_PATH and see if it works..

Thank you,

Asma

On Thu, Jun 11, 2015 at 3:18 PM, Jimmy Yih <jyih@xxxxxxxxxx> wrote:

Hey Asma,

Did you check the linkage with ldd?  For example on my blank RHEL 6.5 AWS VM using gcc 4.4.7:

[jyih@test1 ~]$ ldd /usr/libexec/gcc/x86_64-redhat-linux/4.4.4/cc1
    linux-vdso.so.1 =>  (0x00007fff9b9ff000)
    libmpfr.so.1 => /usr/lib64/libmpfr.so.1 (0x00000033b8400000)
    libgmp.so.3 => /usr/lib64/libgmp.so.3 (0x00000033b8000000)
    libdl.so.2 => /lib64/libdl.so.2 (0x0000003c1e400000)
    libc.so.6 => /lib64/libc.so.6 (0x0000003c1e800000)
    /lib64/ld-linux-x86-64.so.2 (0x0000003c1e000000)

Most likely you should have an empty/broken libmpfr.so linkage.  You can play around with LD_LIBRARY_PATH like so:

## create another libmpfr.so link in a different directory for example

[jyih@test1 ~]$ ls -al /usr/lib64/libmpfr*
lrwxrwxrwx. 1 root root     16 Jun  7  2014 /usr/lib64/libmpfr.so.1 -> libmpfr.so.1.2.0
-rwxr-xr-x. 1 root root 318408 Jun 23  2010 /usr/lib64/libmpfr.so.1.2.0
[jyih@test1 ~]$ ln -s /usr/lib64/libmpfr.so.1.2.0 /tmp/libmpfr.so.1

## show that LD_LIBRARY_PATH is empty and then add new paths

[jyih@test1 ~]$ echo $LD_LIBRARY_PATH

[jyih@test1 ~]$ export LD_LIBRARY_PATH=/tmp:$LD_LIBRARY_PATH

## ldd shows new linking

[jyih@test1 ~]$ ldd /usr/libexec/gcc/x86_64-redhat-linux/4.4.4/cc1
    linux-vdso.so.1 =>  (0x00007fff06dff000)
    libmpfr.so.1 => /tmp/libmpfr.so.1 (0x00000033b8400000)
    libgmp.so.3 => /usr/lib64/libgmp.so.3 (0x00000033b8000000)
    libdl.so.2 => /lib64/libdl.so.2 (0x0000003c1e400000)
    libc.so.6 => /lib64/libc.so.6 (0x0000003c1e800000)
    /lib64/ld-linux-x86-64.so.2 (0x0000003c1e000000)

Hope that helps!

- Jimmy

On Thu, Jun 11, 2015 at 11:44 AM, Asma Riyaz <asmariyaz23@xxxxxxxxx> wrote:

Hi Jimmy,

Here is what I did upon your suggestion;

in bashrc:-

LD_LIBRARY_PATH=/seq/annotation/bio_tools/BOOST/boost_1_46_1/lib

LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/seq/regev_genome_portal/lib

sourced it and then exceuted /.configure as below:

./configure --prefix=/../../DATABASE/postgres

I get the same error log as before.

Asma

On Thu, Jun 11, 2015 at 1:30 PM, Jimmy Yih <jyih@xxxxxxxxxx> wrote:

Hey Asma,

Have you tried running ldd and checking the library linkage?  You might be able to just add the different location to your LD_LIBRARY_PATH as a quick way to get this working.

- Jimmy

On Thu, Jun 11, 2015 at 7:46 AM, Asma Riyaz <asmariyaz23@xxxxxxxxx> wrote:

I have a libmpfr.so.4 under a different location, which setting in configure should I use so that it uses the required library from that directory?

I have used ./configure --prefix=/path/directory LIB=/path/to/libmpfr.so.4 but the config.log still shows that its looking for libmpfr.so.4 under the shared location as before. Any advice will be helpful.

Thank you,

Asma

On Thu, Jun 11, 2015 at 10:34 AM, Geoff Winkless <pgsqladmin@xxxxxxxx> wrote:

On 11 June 2015 at 15:20, Asma Riyaz <asmariyaz23@xxxxxxxxx> wrote:

I have seen an earlier post with gcc errors, however I couldn't figure out what the actual problem here is: is it that libmpfr.so.4 is not found? or gcc needs to be installed fresh?

libmpfr. Unless I've misunderstood, the other errors are simply configure trying to work out which compiler you're running - -V and -qversion simply aren't valid flags to gcc - so those "error" lines are expected result.

Geoff