[gmx-developers] parallel make problems

Erik Marklund erikm at xray.bmc.uu.se
Fri Apr 5 13:49:27 CEST 2013


No. I had an fftw build from before that I reused and instructed gromacs to use.


On 5 Apr 2013, at 13:08, Rossen Apostolov <rossen at kth.se> wrote:

> Hi Erik,
> Are you compiling fftw with the build, i.e. using -DGMX_BUILD_OWN_FFTW ?
> Cheers,
> Rossen
> On 4/5/13 11:55 AM, Erik Marklund wrote:
>> Hi,
>> Building gromacs 4.6.1 failed whenever I issued parallel make, i.e. make -j. I reported this to the cluster admins since I had never seen such behaviour before from gromacs' side, and here's their reply. I can't tell whether gromacs is at fault or the cluster.
>> Erik
>> Begin forwarded message:
>>>  Hi,
>>>> I was compiling gromacs on tintin's login node the other day and it
>>>>   seems that parallel make, i.e. make -j, doesn't work on tintin. I
>>>>   got linker errors that never showed up when make was run serially.
>>>>   I've never encountered such behaviour before.
>>> Without any more information (or being able to look for actual files right now), I'd guess this is a problem with the makefiles rather than the actual make. It seems somewhat unexpected that CMake would create makefiles that aren't safe for parallel building, but it does seem the most likely culprit (assuming it doesn't let developers add rules directly to the makefile to work around problems, I don't remember if that's possible).
>>> That you only see the problem on tintin can likely be explained by timing or other non deterministic factors.
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