[gmx-developers] release-4-6 branch doesn't compile?

Justin Lemkul jalemkul at vt.edu
Sat Nov 17 05:42:50 CET 2012 

Hi All,

Quick question about compiling the latest release-4-6 from git.  It seems that I 
can't get it to compile.  I get the following:

First a warning here
...
[  1%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_arpack.c.o
/home/jalemkul/git/release-4-6/include/thread_mpi/atomic/gcc_x86.h: In function 
‘int tMPI_Atomic_cas(tMPI_Atomic_t*, int, int)’:
/home/jalemkul/git/release-4-6/include/thread_mpi/atomic/gcc_x86.h:135: warning: 
comparison between signed and unsigned integer expressions
[  2%] Building C object src/gmxlib/CMakeFiles/gmx.dir/viewit.c.o
...

and then the actual failure
...
[  9%] Building C object src/gmxlib/CMakeFiles/gmx.dir/mshift.c.o
In file included from /home/jalemkul/git/release-4-6/include/gmx_x86_sse4_1.h:24,
                  from 
/home/jalemkul/git/release-4-6/include/gmx_x86_simd_single.h:35,
                  from /home/jalemkul/git/release-4-6/src/gmxlib/bondfree.c:60:
/usr/lib/gcc/i686-linux-gnu/4.4.5/include/smmintrin.h:32: error: #error "SSE4.1 
instruction set not enabled"
In file included from 
/home/jalemkul/git/release-4-6/include/gmx_x86_simd_single.h:35,
                  from /home/jalemkul/git/release-4-6/src/gmxlib/bondfree.c:60:
/home/jalemkul/git/release-4-6/include/gmx_x86_sse4_1.h:82: error: expected 
declaration specifiers or ‘...’ before ‘__m128’
/home/jalemkul/git/release-4-6/include/gmx_x86_sse4_1.h: In function 
‘gmx_mm_printxmm_ps’:
/home/jalemkul/git/release-4-6/include/gmx_x86_sse4_1.h:86: warning: implicit 
declaration of function ‘_mm_storeu_ps’
/home/jalemkul/git/release-4-6/include/gmx_x86_sse4_1.h:86: error: ‘xmm’ 
undeclared (first use in this function)
/home/jalemkul/git/release-4-6/include/gmx_x86_sse4_1.h:86: error: (Each 
undeclared identifier is reported only once
/home/jalemkul/git/release-4-6/include/gmx_x86_sse4_1.h:86: error: for each 
function it appears in.)
/home/jalemkul/git/release-4-6/include/gmx_x86_sse4_1.h: At top level:
/home/jalemkul/git/release-4-6/include/gmx_x86_sse4_1.h:92: error: expected 
declaration specifiers or ‘...’ before ‘__m128’
/home/jalemkul/git/release-4-6/include/gmx_x86_sse4_1.h: In function 
‘gmx_mm_printxmmsum_ps’:
/home/jalemkul/git/release-4-6/include/gmx_x86_sse4_1.h:96: error: ‘xmm’ 
undeclared (first use in this function)
/home/jalemkul/git/release-4-6/include/gmx_x86_sse4_1.h: At top level:
/home/jalemkul/git/release-4-6/include/gmx_x86_sse4_1.h:102: error: expected 
declaration specifiers or ‘...’ before ‘__m128d’
/home/jalemkul/git/release-4-6/include/gmx_x86_sse4_1.h: In function 
‘gmx_mm_printxmm_pd’:
/home/jalemkul/git/release-4-6/include/gmx_x86_sse4_1.h:106: warning: implicit 
declaration of function ‘_mm_storeu_pd’
/home/jalemkul/git/release-4-6/include/gmx_x86_sse4_1.h:106: error: ‘xmm’ 
undeclared (first use in this function)
/home/jalemkul/git/release-4-6/include/gmx_x86_sse4_1.h: At top level:
/home/jalemkul/git/release-4-6/include/gmx_x86_sse4_1.h:111: error: expected 
declaration specifiers or ‘...’ before ‘__m128d’
/home/jalemkul/git/release-4-6/include/gmx_x86_sse4_1.h: In function 
‘gmx_mm_printxmmsum_pd’:
/home/jalemkul/git/release-4-6/include/gmx_x86_sse4_1.h:115: error: ‘xmm’ 
undeclared (first use in this function)
/home/jalemkul/git/release-4-6/include/gmx_x86_sse4_1.h: At top level:
/home/jalemkul/git/release-4-6/include/gmx_x86_sse4_1.h:121: error: expected 
declaration specifiers or ‘...’ before ‘__m128i’
/home/jalemkul/git/release-4-6/include/gmx_x86_sse4_1.h: In function 
‘gmx_mm_printxmm_epi32’:
/home/jalemkul/git/release-4-6/include/gmx_x86_sse4_1.h:125: warning: implicit 
declaration of function ‘_mm_storeu_si128’
/home/jalemkul/git/release-4-6/include/gmx_x86_sse4_1.h:125: error: ‘__m128i’ 
undeclared (first use in this function)
/home/jalemkul/git/release-4-6/include/gmx_x86_sse4_1.h:125: error: expected 
expression before ‘)’ token
/home/jalemkul/git/release-4-6/include/gmx_x86_sse4_1.h: In function 
‘gmx_mm_check_and_reset_overflow’:
/home/jalemkul/git/release-4-6/include/gmx_x86_sse4_1.h:136: warning: implicit 
declaration of function ‘_mm_getcsr’
/home/jalemkul/git/release-4-6/include/gmx_x86_sse4_1.h:143: warning: implicit 
declaration of function ‘_mm_setcsr’
In file included from 
/home/jalemkul/git/release-4-6/include/gmx_x86_simd_single.h:36,
                  from /home/jalemkul/git/release-4-6/src/gmxlib/bondfree.c:60:
/home/jalemkul/git/release-4-6/include/gmx_math_x86_sse4_1_single.h: At top level:
/home/jalemkul/git/release-4-6/include/gmx_math_x86_sse4_1_single.h:46: error: 
expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘gmx_mm_invsqrt_ps’
/home/jalemkul/git/release-4-6/include/gmx_math_x86_sse4_1_single.h:58: error: 
expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘gmx_mm_sqrt_ps’
/home/jalemkul/git/release-4-6/include/gmx_math_x86_sse4_1_single.h:73: error: 
expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘gmx_mm_inv_ps’
/home/jalemkul/git/release-4-6/include/gmx_math_x86_sse4_1_single.h:83: error: 
expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘gmx_mm_abs_ps’
/home/jalemkul/git/release-4-6/include/gmx_math_x86_sse4_1_single.h:93: error: 
expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘gmx_mm_log_ps’
/home/jalemkul/git/release-4-6/include/gmx_math_x86_sse4_1_single.h:190: error: 
expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘gmx_mm_exp2_ps’
/home/jalemkul/git/release-4-6/include/gmx_math_x86_sse4_1_single.h:248: error: 
expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘gmx_mm_exp_ps’
/home/jalemkul/git/release-4-6/include/gmx_math_x86_sse4_1_single.h:309: error: 
expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘gmx_mm_erf_ps’
/home/jalemkul/git/release-4-6/include/gmx_math_x86_sse4_1_single.h:474: error: 
expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘gmx_mm_erfc_ps’
/home/jalemkul/git/release-4-6/include/gmx_math_x86_sse4_1_single.h:705: error: 
expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘gmx_mm_pmecorrF_ps’
/home/jalemkul/git/release-4-6/include/gmx_math_x86_sse4_1_single.h:783: error: 
expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘gmx_mm_pmecorrV_ps’
/home/jalemkul/git/release-4-6/include/gmx_math_x86_sse4_1_single.h:830: error: 
expected ‘)’ before ‘x’
/home/jalemkul/git/release-4-6/include/gmx_math_x86_sse4_1_single.h:920: error: 
expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘gmx_mm_sin_ps’
/home/jalemkul/git/release-4-6/include/gmx_math_x86_sse4_1_single.h:932: error: 
expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘gmx_mm_cos_ps’
/home/jalemkul/git/release-4-6/include/gmx_math_x86_sse4_1_single.h:941: error: 
expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘gmx_mm_tan_ps’
/home/jalemkul/git/release-4-6/include/gmx_math_x86_sse4_1_single.h:955: error: 
expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘gmx_mm_asin_ps’
/home/jalemkul/git/release-4-6/include/gmx_math_x86_sse4_1_single.h:1024: error: 
expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘gmx_mm_acos_ps’
/home/jalemkul/git/release-4-6/include/gmx_math_x86_sse4_1_single.h:1060: error: 
expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘gmx_mm_atan_ps’
/home/jalemkul/git/release-4-6/include/gmx_math_x86_sse4_1_single.h:1117: error: 
expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘gmx_mm_atan2_ps’
In file included from /home/jalemkul/git/release-4-6/src/gmxlib/bondfree.c:60:
/home/jalemkul/git/release-4-6/include/gmx_x86_simd_single.h:50: error: expected 
‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘gmx_mm_calc_rsq_ps’
/home/jalemkul/git/release-4-6/src/gmxlib/bondfree.c: In function ‘dih_angle_sse’:
/home/jalemkul/git/release-4-6/src/gmxlib/bondfree.c:1229: error: ‘__m128’ 
undeclared (first use in this function)
/home/jalemkul/git/release-4-6/src/gmxlib/bondfree.c:1229: error: expected ‘;’ 
before ‘rijx_SSE’
/home/jalemkul/git/release-4-6/src/gmxlib/bondfree.c:1230: error: expected ‘;’ 
before ‘rkjx_SSE’
/home/jalemkul/git/release-4-6/src/gmxlib/bondfree.c:1231: error: expected ‘;’ 
before ‘rklx_SSE’
/home/jalemkul/git/release-4-6/src/gmxlib/bondfree.c:1232: error: expected ‘;’ 
before ‘mx_SSE’
/home/jalemkul/git/release-4-6/src/gmxlib/bondfree.c:1233: error: expected ‘;’ 
before ‘nx_SSE’
/home/jalemkul/git/release-4-6/src/gmxlib/bondfree.c:1234: error: expected ‘;’ 
before ‘cx_SSE’
/home/jalemkul/git/release-4-6/src/gmxlib/bondfree.c:1235: error: expected ‘;’ 
before ‘cn_SSE’
/home/jalemkul/git/release-4-6/src/gmxlib/bondfree.c:1236: error: expected ‘;’ 
before ‘s_SSE’
/home/jalemkul/git/release-4-6/src/gmxlib/bondfree.c:1237: error: expected ‘;’ 
before ‘phi_SSE’
/home/jalemkul/git/release-4-6/src/gmxlib/bondfree.c:1238: error: expected ‘;’ 
before ‘ipr_SSE’
/home/jalemkul/git/release-4-6/src/gmxlib/bondfree.c:1240: error: expected ‘;’ 
before ‘iprm_SSE’
/home/jalemkul/git/release-4-6/src/gmxlib/bondfree.c:1241: error: expected ‘;’ 
before ‘nrkj2_SSE’
/home/jalemkul/git/release-4-6/src/gmxlib/bondfree.c:1242: error: expected ‘;’ 
before ‘nrkj_m2_SSE’
/home/jalemkul/git/release-4-6/src/gmxlib/bondfree.c:1243: error: expected ‘;’ 
before ‘p_SSE’
/home/jalemkul/git/release-4-6/src/gmxlib/bondfree.c:1244: error: expected ‘;’ 
before ‘fmin_SSE’
/home/jalemkul/git/release-4-6/src/gmxlib/bondfree.c:1253: error: expected ‘;’ 
before ‘tmp’
/home/jalemkul/git/release-4-6/src/gmxlib/bondfree.c:1253: error: ‘rijx_SSE’ 
undeclared (first use in this function)
/home/jalemkul/git/release-4-6/src/gmxlib/bondfree.c:1253: warning: implicit 
declaration of function ‘_mm_load_ps’
/home/jalemkul/git/release-4-6/src/gmxlib/bondfree.c:1253: error: ‘rijy_SSE’ 
undeclared (first use in this function)
/home/jalemkul/git/release-4-6/src/gmxlib/bondfree.c:1253: error: ‘rijz_SSE’ 
undeclared (first use in this function)
/home/jalemkul/git/release-4-6/src/gmxlib/bondfree.c:1253: error: ‘tmp’ 
undeclared (first use in this function)
/home/jalemkul/git/release-4-6/src/gmxlib/bondfree.c:1253: warning: implicit 
declaration of function ‘_MM_TRANSPOSE4_PS’
/home/jalemkul/git/release-4-6/src/gmxlib/bondfree.c:1254: error: expected ‘;’ 
before ‘tmp’
/home/jalemkul/git/release-4-6/src/gmxlib/bondfree.c:1254: error: ‘rkjx_SSE’ 
undeclared (first use in this function)
/home/jalemkul/git/release-4-6/src/gmxlib/bondfree.c:1254: error: ‘rkjy_SSE’ 
undeclared (first use in this function)
/home/jalemkul/git/release-4-6/src/gmxlib/bondfree.c:1254: error: ‘rkjz_SSE’ 
undeclared (first use in this function)
/home/jalemkul/git/release-4-6/src/gmxlib/bondfree.c:1255: error: expected ‘;’ 
before ‘tmp’
/home/jalemkul/git/release-4-6/src/gmxlib/bondfree.c:1255: error: ‘rklx_SSE’ 
undeclared (first use in this function)
/home/jalemkul/git/release-4-6/src/gmxlib/bondfree.c:1255: error: ‘rkly_SSE’ 
undeclared (first use in this function)
/home/jalemkul/git/release-4-6/src/gmxlib/bondfree.c:1255: error: ‘rklz_SSE’ 
undeclared (first use in this function)
/home/jalemkul/git/release-4-6/src/gmxlib/bondfree.c:1257: error: ‘mx_SSE’ 
undeclared (first use in this function)
/home/jalemkul/git/release-4-6/src/gmxlib/bondfree.c:1257: warning: implicit 
declaration of function ‘_mm_sub_ps’
/home/jalemkul/git/release-4-6/src/gmxlib/bondfree.c:1257: warning: implicit 
declaration of function ‘_mm_mul_ps’
/home/jalemkul/git/release-4-6/src/gmxlib/bondfree.c:1257: error: ‘my_SSE’ 
undeclared (first use in this function)
/home/jalemkul/git/release-4-6/src/gmxlib/bondfree.c:1257: error: ‘mz_SSE’ 
undeclared (first use in this function)
/home/jalemkul/git/release-4-6/src/gmxlib/bondfree.c:1261: error: ‘nx_SSE’ 
undeclared (first use in this function)
/home/jalemkul/git/release-4-6/src/gmxlib/bondfree.c:1261: error: ‘ny_SSE’ 
undeclared (first use in this function)
/home/jalemkul/git/release-4-6/src/gmxlib/bondfree.c:1261: error: ‘nz_SSE’ 
undeclared (first use in this function)
/home/jalemkul/git/release-4-6/src/gmxlib/bondfree.c:1265: error: ‘cx_SSE’ 
undeclared (first use in this function)
/home/jalemkul/git/release-4-6/src/gmxlib/bondfree.c:1265: error: ‘cy_SSE’ 
undeclared (first use in this function)
/home/jalemkul/git/release-4-6/src/gmxlib/bondfree.c:1265: error: ‘cz_SSE’ 
undeclared (first use in this function)
/home/jalemkul/git/release-4-6/src/gmxlib/bondfree.c:1269: error: ‘cn_SSE’ 
undeclared (first use in this function)
/home/jalemkul/git/release-4-6/src/gmxlib/bondfree.c:1269: warning: implicit 
declaration of function ‘gmx_mm_sqrt_ps’
/home/jalemkul/git/release-4-6/src/gmxlib/bondfree.c:1269: warning: implicit 
declaration of function ‘_mm_add_ps’
/home/jalemkul/git/release-4-6/src/gmxlib/bondfree.c:1271: error: ‘s_SSE’ 
undeclared (first use in this function)
/home/jalemkul/git/release-4-6/src/gmxlib/bondfree.c:1273: error: ‘phi_SSE’ 
undeclared (first use in this function)
/home/jalemkul/git/release-4-6/src/gmxlib/bondfree.c:1273: warning: implicit 
declaration of function ‘gmx_mm_atan2_ps’
/home/jalemkul/git/release-4-6/src/gmxlib/bondfree.c:1274: warning: implicit 
declaration of function ‘_mm_store_ps’
/home/jalemkul/git/release-4-6/src/gmxlib/bondfree.c:1276: error: ‘ipr_SSE’ 
undeclared (first use in this function)
/home/jalemkul/git/release-4-6/src/gmxlib/bondfree.c:1279: warning: implicit 
declaration of function ‘_mm_movemask_ps’
/home/jalemkul/git/release-4-6/src/gmxlib/bondfree.c:1289: error: ‘iprm_SSE’ 
undeclared (first use in this function)
/home/jalemkul/git/release-4-6/src/gmxlib/bondfree.c:1290: error: ‘iprn_SSE’ 
undeclared (first use in this function)
/home/jalemkul/git/release-4-6/src/gmxlib/bondfree.c:1293: error: expected ‘;’ 
before ‘tmp’
/home/jalemkul/git/release-4-6/src/gmxlib/bondfree.c:1294: error: expected ‘;’ 
before ‘tmp’
/home/jalemkul/git/release-4-6/src/gmxlib/bondfree.c:1296: error: ‘nrkj2_SSE’ 
undeclared (first use in this function)
/home/jalemkul/git/release-4-6/src/gmxlib/bondfree.c:1301: warning: implicit 
declaration of function ‘_mm_max_ps’
/home/jalemkul/git/release-4-6/src/gmxlib/bondfree.c:1301: error: ‘fmin_SSE’ 
undeclared (first use in this function)
/home/jalemkul/git/release-4-6/src/gmxlib/bondfree.c:1302: error: ‘nrkj_1_SSE’ 
undeclared (first use in this function)
/home/jalemkul/git/release-4-6/src/gmxlib/bondfree.c:1302: warning: implicit 
declaration of function ‘gmx_mm_invsqrt_ps’
/home/jalemkul/git/release-4-6/src/gmxlib/bondfree.c:1303: error: ‘nrkj_2_SSE’ 
undeclared (first use in this function)
/home/jalemkul/git/release-4-6/src/gmxlib/bondfree.c:1304: error: ‘nrkj_SSE’ 
undeclared (first use in this function)
/home/jalemkul/git/release-4-6/src/gmxlib/bondfree.c:1308: error: ‘nrkj_m2_SSE’ 
undeclared (first use in this function)
/home/jalemkul/git/release-4-6/src/gmxlib/bondfree.c:1308: warning: implicit 
declaration of function ‘gmx_mm_inv_ps’
/home/jalemkul/git/release-4-6/src/gmxlib/bondfree.c:1309: error: ‘nrkj_n2_SSE’ 
undeclared (first use in this function)
/home/jalemkul/git/release-4-6/src/gmxlib/bondfree.c:1314: error: ‘p_SSE’ 
undeclared (first use in this function)
/home/jalemkul/git/release-4-6/src/gmxlib/bondfree.c:1318: error: ‘q_SSE’ 
undeclared (first use in this function)
/home/jalemkul/git/release-4-6/src/gmxlib/bondfree.c: In function 
‘pdihs_noener_sse’:
/home/jalemkul/git/release-4-6/src/gmxlib/bondfree.c:1672: error: ‘__m128’ 
undeclared (first use in this function)
/home/jalemkul/git/release-4-6/src/gmxlib/bondfree.c:1672: error: expected ‘;’ 
before ‘mdphi_SSE’
/home/jalemkul/git/release-4-6/src/gmxlib/bondfree.c:1721: error: ‘mdphi_SSE’ 
undeclared (first use in this function)
/home/jalemkul/git/release-4-6/src/gmxlib/bondfree.c:1722: warning: implicit 
declaration of function ‘gmx_mm_sincos_ps’
/home/jalemkul/git/release-4-6/src/gmxlib/bondfree.c:1722: error: ‘sin_SSE’ 
undeclared (first use in this function)
/home/jalemkul/git/release-4-6/src/gmxlib/bondfree.c:1722: error: ‘cos_SSE’ 
undeclared (first use in this function)
[  9%] make[2]: *** [src/gmxlib/CMakeFiles/gmx.dir/bondfree.c.o] Error 1
make[2]: *** Waiting for unfinished jobs....
Building C object src/gmxlib/CMakeFiles/gmx.dir/pargs.c.o
make[1]: *** [src/gmxlib/CMakeFiles/gmx.dir/all] Error 2
make: *** [all] Error 2


Given that I'm fairly unfamiliar with the new build system (read: cmake noob), I 
don't know a lot about what you might need to see from my configuration.  I'm 
linking against fftw-3.3.2 and cmake detected SSE4.1 optimization for our system 
(a reasonably new GPU workstation).

$ uname -a
Linux hermes 2.6.35-32-generic #67-Ubuntu SMP Mon Mar 5 19:35:26 UTC 2012 i686 
GNU/Linux

gcc is version 4.4.5.

Please let me know what I need to provide to help diagnose what's going on.  Is 
the optimization not being detected properly?  How would I find that out?

-Justin
-- 
========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================

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