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

Roland Schulz roland at utk.edu
Sat Nov 17 06:20:37 CET 2012 

Hi,

looks like the CFLAGS are missing -msse4.1 . Check whether that is indeed
missing from CMAKE_C_FLAGS (CMakeCache.txt) and add it if it is. Then check
if you delete CMakeCache.txt and rerun cmake, if it doesn't forget to add
it again (to make sure we don't have some bug in cmake).

Roland


On Fri, Nov 16, 2012 at 11:42 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
> 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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> gmx-developers at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-developers
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>
>
>
>
>


-- 
ORNL/UT Center for Molecular Biophysics cmb.ornl.gov
865-241-1537, ORNL PO BOX 2008 MS6309
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