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

Hi everyone...

I think libmpfr.so.4 is being searched for in the /../software/free/Linux/
redhat_6_x86_64/pkgs/gcc_4.9.0/libexec (according to error message) directory
but on our system it is located in /../software/free/Linux/
redhat_6_x86_64/pkgs/gcc_4.9.0/lib

Any idea how I can specify as to which directory should configure refer to
for library directory?

-Thank you,
Asma

On Thu, Jun 11, 2015 at 3:32 PM, Asma Riyaz <asmariyaz23(at)gmail(dot)com> wrote:

> 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
>
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> On Thu, Jun 11, 2015 at 3:18 PM, Jimmy Yih <jyih(at)pivotal(dot)io> 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(at)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(at)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(at)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(at)test1 ~]$ echo $LD_LIBRARY_PATH
>>
>> [jyih(at)test1 ~]$ export LD_LIBRARY_PATH=/tmp:$LD_LIBRARY_PATH
>>
>> ## ldd shows new linking
>> [jyih(at)test1 ~]$ 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(at)gmail(dot)com>
>> 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(at)pivotal(dot)io> 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(at)gmail(dot)com>
>>>> 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(at)geoff(dot)dj>
>>>>> wrote:
>>>>>
>>>>>> On 11 June 2015 at 15:20, Asma Riyaz <asmariyaz23(at)gmail(dot)com> 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
>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>
>