Hi Hsin-Lin, Your problem are caused by a missing header file which is included by the nobonded SSE kernels which is indicated by the first error in your output:
nb_kernel400_ia32_sse.c:22:23: emmintrin.h: No such file or directory This header is needed for SSE and SSE2, but for some reason you don't have it. What platform are you compiling on/for and what compiler are you using? Alternatively, you can turn off acceleration and you'll be able to compile the code, but it will run *much* slower than with the accelerated kernels. -- Szilárd 2011/5/26 Hsin-Lin Chiang <[email protected]>: > Hi, > > I met some problem on installing gromacs 4.5.4 > Below is the log. > I'm soory I can't distinguish the important part and I post all of them. > I'll appreciate for any help. > > Hsin-Lin > ------------- > Making all in include > make[1]: Entering directory `/stathome/jiangsl/src/gromacs-4.5.4/include' > Making all in . > make[2]: Entering directory `/stathome/jiangsl/src/gromacs-4.5.4/include' > make[2]: Nothing to be done for `all-am'. > make[2]: Leaving directory `/stathome/jiangsl/src/gromacs-4.5.4/include' > Making all in types > make[2]: Entering directory > `/stathome/jiangsl/src/gromacs-4.5.4/include/types' > make[2]: Nothing to be done for `all'. > make[2]: Leaving directory > `/stathome/jiangsl/src/gromacs-4.5.4/include/types' > Making all in thread_mpi > make[2]: Entering directory > `/stathome/jiangsl/src/gromacs-4.5.4/include/thread_mpi' > Making all in atomic > make[3]: Entering directory > `/stathome/jiangsl/src/gromacs-4.5.4/include/thread_mpi/atomic' > make[3]: Nothing to be done for `all'. > make[3]: Leaving directory > `/stathome/jiangsl/src/gromacs-4.5.4/include/thread_mpi/atomic' > make[3]: Entering directory > `/stathome/jiangsl/src/gromacs-4.5.4/include/thread_mpi' > make[3]: Nothing to be done for `all-am'. > make[3]: Leaving directory > `/stathome/jiangsl/src/gromacs-4.5.4/include/thread_mpi' > make[2]: Leaving directory > `/stathome/jiangsl/src/gromacs-4.5.4/include/thread_mpi' > make[1]: Leaving directory `/stathome/jiangsl/src/gromacs-4.5.4/include' > Making all in src > make[1]: Entering directory `/stathome/jiangsl/src/gromacs-4.5.4/src' > make all-recursive > make[2]: Entering directory `/stathome/jiangsl/src/gromacs-4.5.4/src' > Making all in gmxlib > make[3]: Entering directory `/stathome/jiangsl/src/gromacs-4.5.4/src/gmxlib' > Making all in nonbonded > make[4]: Entering directory > `/stathome/jiangsl/src/gromacs-4.5.4/src/gmxlib/nonbonded' > Making all in nb_kernel_ia32_sse > make[5]: Entering directory > `/stathome/jiangsl/src/gromacs-4.5.4/src/gmxlib/nonbonded/nb_kernel_ia32_sse' > /bin/sh ../../../../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H > -I. -I../../../../src -I/usr/include/libxml2 -I../../../../include > -DGMXLIBDIR=\"/stathome/jiangsl/soft/gromacs-4.5.4/share/top\" > -I/stathome/jiangsl/soft/fftw-3.2.2/include > -I/stathome/jiangsl/soft/mpich2-1.2.1p1/include -O3 -fomit-frame-pointer > -finline-functions -Wall -Wno-unused -msse2 -funroll-all-loops -std=gnu99 > -pthread -I./include -MT nb_kernel400_ia32_sse.lo -MD -MP -MF > .deps/nb_kernel400_ia32_sse.Tpo -c -o nb_kernel400_ia32_sse.lo > nb_kernel400_ia32_sse.c > cc -DHAVE_CONFIG_H -I. -I../../../../src -I/usr/include/libxml2 > -I../../../../include > -DGMXLIBDIR=\"/stathome/jiangsl/soft/gromacs-4.5.4/share/top\" > -I/stathome/jiangsl/soft/fftw-3.2.2/include > -I/stathome/jiangsl/soft/mpich2-1.2.1p1/include -O3 -fomit-frame-pointer > -finline-functions -Wall -Wno-unused -msse2 -funroll-all-loops -std=gnu99 > -pthread -I./include -MT nb_kernel400_ia32_sse.lo -MD -MP -MF > .deps/nb_kernel400_ia32_sse.Tpo -c nb_kernel400_ia32_sse.c -fPIC -DPIC -o > .libs/nb_kernel400_ia32_sse.o > nb_kernel400_ia32_sse.c:22:23: emmintrin.h: No such file or directory > In file included from nb_kernel400_ia32_sse.c:24: > ../../../../include/gmx_sse2_single.h:39:34: emmintrin.h: No such file or > directory > In file included from nb_kernel400_ia32_sse.c:24: > ../../../../include/gmx_sse2_single.h:128: syntax error before "__m128i" > ../../../../include/gmx_sse2_single.h: In function `printxmmi': > ../../../../include/gmx_sse2_single.h:132: warning: implicit declaration of > function `_mm_storeu_si128' > ../../../../include/gmx_sse2_single.h:132: `__m128i' undeclared (first use > in this function) > ../../../../include/gmx_sse2_single.h:132: (Each undeclared identifier is > reported only once > ../../../../include/gmx_sse2_single.h:132: for each function it appears in.) > ../../../../include/gmx_sse2_single.h:132: syntax error before ')' token > ../../../../include/gmx_sse2_single.h:133: `s' undeclared (first use in this > function) > ../../../../include/gmx_sse2_single.h: In function `gmx_mm_log_ps': > ../../../../include/gmx_sse2_single.h:215: warning: implicit declaration of > function `_mm_set_epi32' > ../../../../include/gmx_sse2_single.h:215: can't convert between vector > values of different size > ../../../../include/gmx_sse2_single.h:216: syntax error before "expbase_m1" > ../../../../include/gmx_sse2_single.h:234: `__m128i' undeclared (first use > in this function) > ../../../../include/gmx_sse2_single.h:234: syntax error before "iexp" > ../../../../include/gmx_sse2_single.h:242: `iexp' undeclared (first use in > this function) > ../../../../include/gmx_sse2_single.h:243: warning: implicit declaration of > function `_mm_srli_epi32' > ../../../../include/gmx_sse2_single.h:244: warning: implicit declaration of > function `_mm_sub_epi32' > ../../../../include/gmx_sse2_single.h:244: `expbase_m1' undeclared (first > use in this function) > ../../../../include/gmx_sse2_single.h:254: warning: implicit declaration of > function `_mm_add_epi32' > ../../../../include/gmx_sse2_single.h:278: warning: implicit declaration of > function `_mm_cvtepi32_ps' > ../../../../include/gmx_sse2_single.h:278: incompatible types in assignment > In file included from nb_kernel400_ia32_sse.c:24: > ../../../../include/gmx_sse2_single.h: In function `gmx_mm_exp_ps': > ../../../../include/gmx_sse2_single.h:329: syntax error before "expbase" > ../../../../include/gmx_sse2_single.h:339: `__m128i' undeclared (first use > in this function) > ../../../../include/gmx_sse2_single.h:339: syntax error before "iexppart" > ../../../../include/gmx_sse2_single.h:346: `iexppart' undeclared (first use > in this function) > ../../../../include/gmx_sse2_single.h:346: warning: implicit declaration of > function `_mm_cvtps_epi32' > ../../../../include/gmx_sse2_single.h:351: incompatible types in assignment > ../../../../include/gmx_sse2_single.h:353: warning: implicit declaration of > function `_mm_slli_epi32' > ../../../../include/gmx_sse2_single.h:353: `expbase' undeclared (first use > in this function) > In file included from nb_kernel400_ia32_sse.c:24: > ../../../../include/gmx_sse2_single.h: In function `gmx_mm_sincos_ps': > ../../../../include/gmx_sse2_single.h:391: syntax error before > "_sincosf_izero" > ../../../../include/gmx_sse2_single.h:392: syntax error before > "_sincosf_ione" > ../../../../include/gmx_sse2_single.h:393: syntax error before > "_sincosf_itwo" > ../../../../include/gmx_sse2_single.h:394: syntax error before > "_sincosf_ithree" > ../../../../include/gmx_sse2_single.h:405: warning: implicit declaration of > function `_mm_set1_epi32' > ../../../../include/gmx_sse2_single.h:405: can't convert between vector > values of different size > ../../../../include/gmx_sse2_single.h:406: can't convert between vector > values of different size > ../../../../include/gmx_sse2_single.h:420: `__m128i' undeclared (first use > in this function) > ../../../../include/gmx_sse2_single.h:420: syntax error before "_sincosf_q" > ../../../../include/gmx_sse2_single.h:436: `_sincosf_q' undeclared (first > use in this function) > ../../../../include/gmx_sse2_single.h:436: warning: implicit declaration of > function `_mm_cvttps_epi32' > ../../../../include/gmx_sse2_single.h:437: incompatible types in assignment > ../../../../include/gmx_sse2_single.h:439: `_sincosf_offsetSin' undeclared > (first use in this function) > ../../../../include/gmx_sse2_single.h:439: warning: implicit declaration of > function `_mm_and_si128' > ../../../../include/gmx_sse2_single.h:439: `_sincosf_ithree' undeclared > (first use in this function) > ../../../../include/gmx_sse2_single.h:440: `_sincosf_offsetCos' undeclared > (first use in this function) > ../../../../include/gmx_sse2_single.h:440: `_sincosf_ione' undeclared (first > use in this function) > ../../../../include/gmx_sse2_single.h:468: warning: implicit declaration of > function `_mm_cmpeq_epi32' > ../../../../include/gmx_sse2_single.h:468: `_sincosf_izero' undeclared > (first use in this function) > ../../../../include/gmx_sse2_single.h:468: can't convert between vector > values of different size > ../../../../include/gmx_sse2_single.h:469: can't convert between vector > values of different size > ../../../../include/gmx_sse2_single.h:474: `_sincosf_itwo' undeclared (first > use in this function) > ../../../../include/gmx_sse2_single.h:474: can't convert between vector > values of different size > ../../../../include/gmx_sse2_single.h:478: can't convert between vector > values of different size > In file included from nb_kernel400_ia32_sse.c:24: > ../../../../include/gmx_sse2_single.h: In function `gmx_mm_asin_ps': > ../../../../include/gmx_sse2_single.h:506: can't convert between vector > values of different size > In file included from nb_kernel400_ia32_sse.c:24: > ../../../../include/gmx_sse2_single.h: In function `gmx_mm_acos_ps': > ../../../../include/gmx_sse2_single.h:574: can't convert between vector > values of different size > ../../../../include/gmx_sse2_single.h: In function `gmx_mm_atan_ps': > ../../../../include/gmx_sse2_single.h:611: can't convert between vector > values of different size > nb_kernel400_ia32_sse.c: In function `nb_kernel400_ia32_sse': > nb_kernel400_ia32_sse.c:93: can't convert between vector values of different > size > nb_kernel400_ia32_sse.c:94: can't convert between vector values of different > size > nb_kernel400_ia32_sse.c:95: can't convert between vector values of different > size > nb_kernel400_ia32_sse.c:97: `__m128i' undeclared (first use in this > function) > nb_kernel400_ia32_sse.c:97: syntax error before "n0" > nb_kernel400_ia32_sse.c:217: `n0' undeclared (first use in this function) > nb_kernel400_ia32_sse.c:218: `n0B' undeclared (first use in this function) > nb_kernel400_ia32_sse.c:219: incompatible type for argument 2 of > `_mm_sub_ps' > nb_kernel400_ia32_sse.c:220: incompatible type for argument 2 of > `_mm_sub_ps' > nb_kernel400_ia32_sse.c:221: `nnn' undeclared (first use in this function) > nb_kernel400_ia32_sse.c:222: `nnnB' undeclared (first use in this function) > nb_kernel400_ia32_sse.c:225: warning: implicit declaration of function > `_mm_cvtsi128_si32' > nb_kernel400_ia32_sse.c:225: warning: implicit declaration of function > `_mm_srli_si128' > nb_kernel400_ia32_sse.c:337: incompatible type for argument 2 of > `_mm_sub_ps' > nb_kernel400_ia32_sse.c:452: incompatible type for argument 2 of > `_mm_sub_ps' > make[5]: *** [nb_kernel400_ia32_sse.lo] Error 1 > make[5]: Leaving directory > `/stathome/jiangsl/src/gromacs-4.5.4/src/gmxlib/nonbonded/nb_kernel_ia32_sse' > make[4]: *** [all-recursive] Error 1 > make[4]: Leaving directory > `/stathome/jiangsl/src/gromacs-4.5.4/src/gmxlib/nonbonded' > make[3]: *** [all-recursive] Error 1 > make[3]: Leaving directory `/stathome/jiangsl/src/gromacs-4.5.4/src/gmxlib' > make[2]: *** [all-recursive] Error 1 > make[2]: Leaving directory `/stathome/jiangsl/src/gromacs-4.5.4/src' > make[1]: *** [all] Error 2 > make[1]: Leaving directory `/stathome/jiangsl/src/gromacs-4.5.4/src' > make: *** [all-recursive] Error 1 > > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
