[gmx-users] Error of installing gromacs v4.5.4

[Szilárd Páll]

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 <jiangsl at phys.sinica.edu.tw>:
> 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
>
> --
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