[gmx-users] Installing GROMACS 4.6.7 on Intel Cluster

[Szilárd Páll]

There is something *very* weird happening here, it looks like cmake
ends up in some kind of recursion and just before it crashes it is
installing in a directory which contains '/gromacs' about 300 times.

My first guess is that you are installing in the same directory where
your build (and source tree?) is. Is that the case?

--
Szilárd


On Mon, Nov 10, 2014 at 12:31 AM, Agnivo Gosai
<agnivogromacs14 at gmail.com> wrote:
> Dear Users
>
> Dr.Szilard : I searched in the web regarding the correct syntax and as you
> wrote in the last mail , ran it again.
>
> The generated log file is huge. 260 MB. So I am sending a Google Drive
> link. If possible kindly check and suggest further.
>
>
>
> ---------- Forwarded message ----------
> From: "Szilárd Páll" <pall.szilard at gmail.com>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Cc: Discussion list for GROMACS users <
> gromacs.org_gmx-users at maillist.sys.kth.se>
> Date: Sun, 9 Nov 2014 23:16:23 +0100
> Subject: Re: [gmx-users] Installing GROMACS 4.6.7 on Intel Cluster
> On Sun, Nov 9, 2014 at 9:17 PM, Szilárd Páll <pall.szilard at gmail.com> wrote:
>> That looks like it could actually be a compiler/linker or cmake crash.
>> Could you run:
>> $ make
>> and then
>> $ make install VERBOSE=1 2&1 | tee make-install.out
>
> There is a typo in the above command! Here's the correct version:
> $ make install VERBOSE=1 2>&1 | tee make-install.out
>
>> and share the resulting make-install.out file (use pastebin or similar).
>>
>> Cheers,
>> --
>> Szilárd
>>
>>
>> On Sun, Nov 9, 2014 at 8:21 PM, Agnivo Gosai <agnivogromacs14 at gmail.com>
> wrote:
>>> Dear Users
>>>
>>> I have tried installing both versions 4.6.5 and 4.6.7 in the Intel
> cluster
>>> at my university. I have tried with both Intel compilers as well as GNU
>>> compilers. During installation I have checked that Cmake is automatically
>>> detecting Openmp and AVX 256.
>>>
>>> Also , I keep -DGMX_BUILD_OWN_FFTW=ON. However , still at the last step
> of
>>> make install I am getting the following error :-
>>>
>>> terminate called after throwing an instance of 'std::bad_alloc'
>>> what():  std::bad_alloc
>>> make: *** [install] Aborted
>>>
>>> I searched in the web but could not find such an error associated with
>>> GROMACS installation.
>>>
>>> Then I separately tried installing "mdrun" only from version 4.6.5 and I
>>> could do that. I also checked that it operates as follows :- ./mdrun.
>>>
>>> However I need to install the full package.
>>>
>>> Kindly help with suggestions.
>  make-install.out
> <https://docs.google.com/file/d/0B-U8uULVZjfRWWhWTDY3cU1LSEk/edit?usp=drive_web>
>
> Thanks & Regards
> Agnivo Gosai
> Grad Student, Iowa State University.
> --
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