[gmx-users] Installing GROMACS 4.6.7 on Intel Cluster
pall.szilard at gmail.com
Mon Nov 10 00:52:48 CET 2014
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?
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).
>> 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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