[gmx-users] Installing GROMACS 4.6.7 on Intel Cluster

[Szilárd Páll]

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.
>>
>>
>> ---------- 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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