[gmx-users] Installing GROMACS 4.6.7 on Intel Cluster

[Szilárd Páll]

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

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.
>
>
> ---------- Forwarded message ----------
> From: suresh kannan <sureshcbt at gmail.com>
> To: gmx-users at gromacs.org
> Cc:
> Date: Sun, 9 Nov 2014 22:46:29 +0900
> Subject: Re: [gmx-users] Installing GROMACS 4.6.7 on Intel Cluster
>>>>I am thinking of using "gcc" and "g++" now. Kindly provide further
> suggestions.
>
> http://hpc.ucla.edu/hoffman2/software/compilers
>
> http://lmgtfy.com/?q=difference+between+gcc+and+g%2B%2B
>
> http://lmgtfy.com/?q=gcc+compiler+installation+linux
>
>
> <
> https://mail.google.com/mail/u/0/?ui=2&ik=4d6c0a5051&view=att&th=149643f024d7d537&attid=0.1&disp=safe&realattid=f_i1wzdfrg0&zw
>>
>
> On Sun, Nov 9, 2014 at 9:42 AM, Agnivo Gosai <agnivogromacs14 at gmail.com>
> wrote:
>
>> Dear Users
>>
>> I figured out from the trailing mails as to how to use the "new installed
>> version of CMAKE" for installing GROMACS
>>
>> I used  -DGMX_BUILD_OWN_FFTW=ON  -DCMAKE_INSTALL_PREFIX=.......
> .. .
>> By default I think "icc" and "icpc" compilers were chosen.
>>
>> This step progressed smoothly. So , next I issued the command : "make".
>> This step also completed without any error messages.
>>
>> However "make install" did not finish as expected. The installation
> process
>> looked like a never ending process. Ultimately the following error message
>> came up :
>>
>> terminate called after throwing an instance of 'std::bad_alloc'
>>   what():  std::bad_alloc
>> make: *** [install] Aborted
>>
>> I do not understand what to do next. I am thinking of using "gcc" and
> "g++"
>> now. Kindly provide further suggestions.
>>
>>
>>
>>
> ------------------------------------------------------------------------------------------------------------------------------------
>>
>
>
> Thanks & Regards
> Agnivo Gosai
> Grad Student, Iowa State University.
> --
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