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CCPEM  August 2018

CCPEM August 2018

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Subject:

Re: Relion 3 compile on MAC chokes on malloc_trim

From:

Takanori Nakane <[log in to unmask]>

Reply-To:

Takanori Nakane <[log in to unmask]>

Date:

Tue, 7 Aug 2018 12:52:31 +0100

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (69 lines)

Hi Susan,

I think you can comment out malloc_trim() from the code.
It is only there to save memory.

Please note that we do not officially support compilation on Mac OS X.

Best regards,

Takanori Nakane

> Compiling Relion3 on MacBook (High Sierra 10.13.6), relion has pulled
its
> own fftw libraries:
> using gcc versions between 5.4 and 7.3 / openmpi 3.1.1  consistently
gives
> two errors:
> 1. cmake notes that function sincos not found but then says __sincos
found
> and completes, however make fails with function "sincos" not declared in
> ctf.h .... if edit this to __sincos in ctf.h compilation proceeds past
> this point
> 2. make fails
> /src/relion-3.0_beta/src/jaz/motion/motion_param_estimator.cpp: In
member fu
> nction ?void MotionParamEstimator::prepAlignment()?:
> /src/relion-3.0_beta/src/jaz/motion/motion_param_estimator.cpp:499:5:
error:
>  ?malloc_trim? was not declared in this scope
>      malloc_trim(0);
>      ^~~~~~~~~~~
> /src/relion-3.0_beta/src/jaz/motion/motion_param_estimator.cpp:499:5:
note:
> suggested alternative: ?malloc?
>      malloc_trim(0);
>      ^~~~~~~~~~~
>      malloc
> [ 56%] Building CXX object
> src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/two_hyperparameter_fit.cpp.o
> [ 56%] Building C object
> src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyev2.c.o
> make[2]: ***
> [src/apps/CMakeFiles/relion_lib.dir/__/jaz/motion/motion_param_estimator.cpp.o]
> Error 1
> make[2]: *** Waiting for unfinished jobs....
> [ 57%] Building C object
> src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevc3.c.o
> make[1]: *** [src/apps/CMakeFiles/relion_lib.dir/all] Error 2
> this seems to stink of some compiler mis-match as the same code compiles
> happily on our cluster
> any ideas?
> thanks
> Susan
> Prof. Susan M. Lea,  FMedSci                      tel: +44 1865 275181
> ------------------------------------------------------------------------------------------
> Director of the Central Oxford Structural Microscopy and Imaging Centre
&
> Professor of Microbiology
> Sir William Dunn School of Pathology, Oxford OX1 3RE Professorial Fellow
@
> WadhamCollege
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