Re: [gmx-users] Error while compiling GROMACS 2018

2018-01-15 Thread Paul Bauer 

Hello,

it seems like you have some manually copied files in your source tree. 
Please try to remove them and build again.
The line you see in the first error message was changed during the 
recent testing (listed-forces/bonded.cpp) and is causing the error in 
your local copy (listed-forces/bonded_2.cpp).


Cheers

Paul

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[gmx-users] Error while compiling GROMACS 2018

2018-01-12 Thread Yongchul Chung 
Hi,

I am trying to install the latest release of GROMACS 2018 on Mac OS X
HighSierrra and ran into the following error message.

cmake worked without errors so this looks strange.

Any help would be appreciated.

Greg


ygchung@Yongchuls-MacBook-Pro:*~/Desktop/codes/gromacs/build*$ make

[  1%] Built target fftwBuild

[  2%] Built target tng_io_obj

[  2%] *Generating git version information*

[  2%] Built target git-version-info

[  2%] Built target tng_io_zlib

[  2%] Building CXX object
src/gromacs/CMakeFiles/libgromacs.dir/listed-forces/bonded_2.cpp.o

*/Users/ygchung/Desktop/codes/gromacs/src/gromacs/listed-forces/bonded
2.cpp:985:20: **error: **expected '(' for function-style cast or type
construction*

GMX_ALIGNED(int, GMX_SIMD_REAL_WIDTH)ai[GMX_SIMD_REAL_WIDTH];

*~~~^*

*/Users/ygchung/Desktop/codes/gromacs/src/gromacs/listed-forces/bonded
2.cpp:986:20: **error: **expected '(' for function-style cast or type
construction*

GMX_ALIGNED(int, GMX_SIMD_REAL_WIDTH)aj[GMX_SIMD_REAL_WIDTH];

*~~~^*

*/Users/ygchung/Desktop/codes/gromacs/src/gromacs/listed-forces/bonded
2.cpp:987:20: **error: **expected '(' for function-style cast or type
construction*

GMX_ALIGNED(int, GMX_SIMD_REAL_WIDTH)ak[GMX_SIMD_REAL_WIDTH];

*~~~^*

*/Users/ygchung/Desktop/codes/gromacs/src/gromacs/listed-forces/bonded
2.cpp:988:17: **error: **unexpected type name 'real': expected expression*

GMX_ALIGNED(real, GMX_SIMD_REAL_WIDTH)   coeff[2*GMX_SIMD_REAL_WIDTH];

*^*

*/Users/ygchung/Desktop/codes/gromacs/src/gromacs/listed-forces/bonded
2.cpp:1008:17: **error: **unexpected type name 'real': expected expression*

GMX_ALIGNED(real, GMX_SIMD_REAL_WIDTH)
pbc_simd[9*GMX_SIMD_REAL_WIDTH];

*^*

*/Users/ygchung/Desktop/codes/gromacs/src/gromacs/listed-forces/bonded
2.cpp:1010:23: **error: **use of undeclared identifier 'pbc_simd'*

set_pbc_simd(pbc, pbc_simd);

*  ^*

*/Users/ygchung/Desktop/codes/gromacs/src/gromacs/listed-forces/bonded
2.cpp:1022:13: **error: **use of undeclared identifier 'ai'*

ai[s] = forceatoms[iu+1];

*^*

*/Users/ygchung/Desktop/codes/gromacs/src/gromacs/listed-forces/bonded
2.cpp:1023:13: **error: **use of undeclared identifier 'aj'*

aj[s] = forceatoms[iu+2];

*^*

*/Users/ygchung/Desktop/codes/gromacs/src/gromacs/listed-forces/bonded
2.cpp:1024:13: **error: **use of undeclared identifier 'ak'*

ak[s] = forceatoms[iu+3];

*^*

*/Users/ygchung/Desktop/codes/gromacs/src/gromacs/listed-forces/bonded
2.cpp:1029:17: **error: **use of undeclared identifier 'coeff'*

coeff[s] =
forceparams[type].harmonic.krA;

*^*

*/Users/ygchung/Desktop/codes/gromacs/src/gromacs/listed-forces/bonded
2.cpp:1030:17: **error: **use of undeclared identifier 'coeff'*

coeff[GMX_SIMD_REAL_WIDTH+s] =
forceparams[type].harmonic.rA;

*^*

*/Users/ygchung/Desktop/codes/gromacs/src/gromacs/listed-forces/bonded
2.cpp:1039:17: **error: **use of undeclared identifier 'coeff'*

coeff[s] = 0;

*^*

*/Users/ygchung/Desktop/codes/gromacs/src/gromacs/listed-forces/bonded
2.cpp:1040:17: **error: **use of undeclared identifier 'coeff'*

coeff[GMX_SIMD_REAL_WIDTH+s] = 0;

*^*

*/Users/ygchung/Desktop/codes/gromacs/src/gromacs/listed-forces/bonded
2.cpp:1045:68: **error: **use of undeclared identifier 'ai'*

gatherLoadUTranspose<3>(reinterpret_cast(x), ai,
_S, _S, _S);

*   ^*

*/Users/ygchung/Desktop/codes/gromacs/src/gromacs/listed-forces/bonded
2.cpp:1046:68: **error: **use of undeclared identifier 'aj'*

gatherLoadUTranspose<3>(reinterpret_cast(x), aj,
_S, _S, _S);

*   ^*

*/Users/ygchung/Desktop/codes/gromacs/src/gromacs/listed-forces/bonded
2.cpp:1047:68: **error: **use of undeclared identifier 'ak'*

gatherLoadUTranspose<3>(reinterpret_cast(x), ak,
_S, _S, _S);

*   ^*

*/Users/ygchung/Desktop/codes/gromacs/src/gromacs/listed-forces/bonded
2.cpp:1055:36: **error: **use of undeclared identifier 'coeff'*

k_S   = load(coeff);

*   ^*

*/Users/ygchung/Desktop/codes/gromacs/src/gromacs/listed-forces/bonded
2.cpp:1056:36: **error: **use of undeclared identifier 'coeff'*

theta0_S  = load(coeff+GMX_SIMD_REAL_WIDTH) * deg2rad_S;

*   ^*

*/Users/ygchung/Desktop/codes/gromacs/src/gromacs/listed-forces/bonded
2.cpp:1058:56: **error: **use of undeclared identifier 'pbc_simd'*

pbc_correct_dx_simd(_S, _S, _S, pbc_simd);

*   ^*