[gmx-users] Installing GROMACS 4.6.7 on Intel Cluster

Agnivo Gosai agnivogromacs14 at gmail.com
Mon Nov 10 00:32:02 CET 2014

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>
>> Dear Users
>> I have tried installing both versions 4.6.5 and 4.6.7 in the Intel
>> 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
>> 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.​
Thanks & Regards
Agnivo Gosai
Grad Student, Iowa State University.

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