[GE users] How do compile gridengine?

Rayson Ho rayrayson at gmail.com
Wed Dec 26 20:58:18 GMT 2007


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On Dec 26, 2007 3:14 PM, tmac <tmacmd at gmail.com> wrote:
> I have having the worst luck compiling the software...
>
> Trying to compile on RHEL 5.1
> Am I missing an RPM for compilation? What could be missing?
> Thanks
>
> I got the source sge-V60u7_1_TAG-src.tar file, un-tar'd it.
> cd gridengine/source
> ./aimk -only-depend
> ./scripts/zerodepend
> ./aimk depend
> ./aimk

Happy hoildays,

It's likely to be a problem with your java path and settings. You can
either adjust them in aimk.site, or invoke ./aimk as:

./aimk -no-java -no-jni

Rayson




>
> Fails with:
> ./aimk
> making in LINUXAMD64_26/ for LINUXAMD64 at host moss-tmac.tycho.ncsc.mil
> _________C_O_R_E__S_Y_S_T_E_M_____________
> gcc -O3 -Wall -Werror -Wstrict-prototypes -D__GRIDENGINE_FD_SETSIZE=8192
> -DLINUX -DLINUXAMD64 -DLINUXAMD64_26 -D_GNU_SOURCE -DGETHOSTBYNAME_R6
> -DGETHOSTBYADDR_R8  -DLOAD_OPENSSL -I/vol2/SW/db- 4.2.52/lx26-amd64/include/
> -DTARGET_64BIT -DQCONF_FLATFILE  -DSPOOLING_dynamic -DSECURE
> -I/vol2/tools/SW/openssl-0.9.7e/lx26-amd64/include -DCOMPILE_DC
> -D__SGE_COMPILE_WITH_GETTEXT__  -D__SGE_NO_USERMAPPING__ -I../common
> -I../libs -I../libs/uti -I../libs/gdi -I../libs/japi -I../libs/sgeobj
> -I../libs/cull -I../libs/rmon -I../libs/comm -I../libs/comm/lists
> -I../libs/sched -I../libs/evc -I../libs/evm -I../libs/mir -I../libs/lck
> -I../daemons/common -I../daemons/qmaster -I../daemons/execd
> -I../daemons/schedd -I../clients/common -I. -I/usr/include
> -I/usr/include/linux -fPIC -c ../libs/sgeobj/config.c
> In file included from /usr/include/_G_config.h:44,
>                  from /usr/include/libio.h:32,
>                  from /usr/include/stdio.h:72,
>                  from ../libs/sgeobj/config.c:33:
> /usr/include/gconv.h:72: error: expected declaration specifiers or '...'
> before 'size_t'
> /usr/include/gconv.h:88: error: expected declaration specifiers or '...'
> before 'size_t'
> /usr/include/gconv.h:97: error: expected declaration specifiers or '...'
> before 'size_t'
> /usr/include/gconv.h:174: error: expected specifier-qualifier-list before
> 'size_t'
> In file included from /usr/include/stdio.h:72,
>                  from ../libs/sgeobj/config.c:33:
> /usr/include/libio.h:329: error: expected specifier-qualifier-list before
> 'size_t'
> /usr/include/libio.h:361: error: expected declaration specifiers or '...'
> before 'size_t'
> /usr/include/libio.h:370: error: expected declaration specifiers or '...'
> before 'size_t'
> /usr/include/libio.h:486: error: expected '=', ',', ';', 'asm' or
> '__attribute__' before '_IO_sgetn'
> In file included from ../libs/sgeobj/config.c:33:
> /usr/include/stdio.h:291: error: expected declaration specifiers or '...'
> before 'size_t'
> /usr/include/stdio.h:296: error: expected declaration specifiers or '...'
> before 'size_t'
> /usr/include/stdio.h:308: error: expected declaration specifiers or '...'
> before 'size_t'
> /usr/include/stdio.h:315: error: expected declaration specifiers or '...'
> before 'size_t'
> /usr/include/stdio.h:357: error: expected declaration specifiers or '...'
> before 'size_t'
> /usr/include/stdio.h:359: error: format string argument not a string type
> /usr/include/stdio.h:361: error: expected declaration specifiers or '...'
> before 'size_t'
> /usr/include/stdio.h:363: error: format string argument not a string type
> /usr/include/stdio.h:567: error: expected declaration specifiers or '...'
> before 'size_t'
> /usr/include/stdio.h:570: error: expected declaration specifiers or '...'
> before 'size_t'
> /usr/include/stdio.h:580: error: expected declaration specifiers or '...'
> before 'size_t'
> /usr/include/stdio.h:610: error: expected '=', ',', ';', 'asm' or
> '__attribute__' before 'fread'
> /usr/include/stdio.h:616: error: expected '=', ',', ';', 'asm' or
> '__attribute__' before 'fwrite'
> /usr/include/stdio.h:638: error: expected '=', ',', ';', 'asm' or
> '__attribute__' before 'fread_unlocked'
> /usr/include/stdio.h:640: error: expected '=', ',', ';', 'asm' or
> '__attribute__' before 'fwrite_unlocked'
> In file included from /usr/include/stdio.h:835,
>                  from ../libs/sgeobj/config.c:33:
> /usr/include/bits/stdio.h:112: error: expected declaration specifiers or
> '...' before 'size_t'
> /usr/include/bits/stdio.h: In function 'getline':
> /usr/include/bits/stdio.h:114: error: '__n' undeclared (first use in this
> function)
> /usr/include/bits/stdio.h:114: error: (Each undeclared identifier is
> reported only once
> /usr/include/bits/stdio.h:114: error: for each function it appears in.)
> /usr/include/bits/stdio.h:114: error: too many arguments to function
> '__getdelim'
> In file included from ../libs/sgeobj/config.c:34:
> /usr/include/string.h: At top level:
> /usr/include/string.h:39: error: expected declaration specifiers or '...'
> before 'size_t'
> /usr/include/string.h:43: error: expected declaration specifiers or '...'
> before 'size_t'
> /usr/include/string.h:52: error: expected declaration specifiers or '...'
> before 'size_t'
> /usr/include/string.h:59: error: expected declaration specifiers or '...'
> before 'size_t'
> /usr/include/string.h:62: error: expected declaration specifiers or '...'
> before 'size_t'
> /usr/include/string.h:66: error: expected declaration specifiers or '...'
> before 'size_t'
> /usr/include/string.h:77: error: expected declaration specifiers or '...'
> before 'size_t'
> /usr/include/string.h:88: error: expected declaration specifiers or '...'
> before 'size_t'
> /usr/include/string.h:96: error: expected declaration specifiers or '...'
> before 'size_t'
> /usr/include/string.h:102: error: expected declaration specifiers or '...'
> before 'size_t'
> /usr/include/string.h:109: error: expected '=', ',', ';', 'asm' or
> '__attribute__' before 'strxfrm'
> In file included from ../libs/sgeobj/config.c:34:
> /usr/include/string.h:124: error: expected '=', ',', ';', 'asm' or
> '__attribute__' before 'strxfrm_l'
> /usr/include/string.h:138: error: expected declaration specifiers or '...'
> before 'size_t'
> /usr/include/string.h:184: error: expected '=', ',', ';', 'asm' or
> '__attribute__' before 'strcspn'
> /usr/include/string.h:188: error: expected '=', ',', ';', 'asm' or
> '__attribute__' before 'strspn'
> /usr/include/string.h:225: error: expected declaration specifiers or '...'
> before 'size_t'
> /usr/include/string.h:226: error: expected declaration specifiers or '...'
> before 'size_t'
> /usr/include/string.h:227: error: nonnull argument with out-of-range operand
> number (argument 1, operand 3)
> /usr/include/string.h:232: error: expected declaration specifiers or '...'
> before 'size_t'
> /usr/include/string.h:235: error: expected declaration specifiers or '...'
> before 'size_t'
> /usr/include/string.h:242: error: expected '=', ',', ';', 'asm' or
> '__attribute__' before 'strlen'
> /usr/include/string.h:249: error: expected '=', ',', ';', 'asm' or
> '__attribute__' before 'strnlen'
> /usr/include/string.h:281: error: expected declaration specifiers or '...'
> before 'size_t'
> /usr/include/string.h:288: error: expected declaration specifiers or '...'
> before 'size_t'
> /usr/include/string.h:292: error: expected declaration specifiers or '...'
> before 'size_t'
> /usr/include/string.h:296: error: expected declaration specifiers or '...'
> before 'size_t'
> /usr/include/string.h:299: error: expected declaration specifiers or '...'
> before 'size_t'
> /usr/include/string.h:329: error: expected declaration specifiers or '...'
> before 'size_t'
> /usr/include/string.h:341: error: expected declaration specifiers or '...'
> before 'size_t'
> /usr/include/string.h:342: error: nonnull argument with out-of-range operand
> number (argument 1, operand 4)
> /usr/include/string.h:370: error: expected declaration specifiers or '...'
> before 'size_t'
> /usr/include/string.h:373: error: expected declaration specifiers or '...'
> before 'size_t'
> /usr/include/string.h:380: error: expected declaration specifiers or '...'
> before 'size_t'
> In file included from /usr/include/string.h:417,
>                  from ../libs/sgeobj/config.c:34:
> /usr/include/bits/string2.h:969: error: expected '=', ',', ';', 'asm' or
> '__attribute__' before '__strcspn_c1'
>  /usr/include/bits/string2.h:971: error: expected '=', ',', ';', 'asm' or
> '__attribute__' before '__strcspn_c1'
> /usr/include/bits/string2.h:979: error: expected '=', ',', ';', 'asm' or
> '__attribute__' before '__strcspn_c2'
> /usr/include/bits/string2.h:982: error: expected '=', ',', ';', 'asm' or
> '__attribute__' before '__strcspn_c2'
> /usr/include/bits/string2.h:991: error: expected '=', ',', ';', 'asm' or
> '__attribute__' before '__strcspn_c3'
> /usr/include/bits/string2.h:994: error: expected '=', ',', ';', 'asm' or
> '__attribute__' before '__strcspn_c3'
> /usr/include/bits/string2.h:1045: error: expected '=', ',', ';', 'asm' or
> '__attribute__' before '__strspn_c1'
> /usr/include/bits/string2.h:1047: error: expected '=', ',', ';', 'asm' or
> '__attribute__' before '__strspn_c1'
> /usr/include/bits/string2.h:1056: error: expected '=', ',', ';', 'asm' or
> '__attribute__' before '__strspn_c2'
> /usr/include/bits/string2.h:1059: error: expected '=', ',', ';', 'asm' or
> '__attribute__' before '__strspn_c2'
> /usr/include/bits/string2.h:1068: error: expected '=', ',', ';', 'asm' or
> '__attribute__' before '__strspn_c3'
> /usr/include/bits/string2.h:1071: error: expected '=', ',', ';', 'asm' or
> '__attribute__' before '__strspn_c3'
> /usr/include/bits/string2.h: In function '__strpbrk_c2':
> /usr/include/bits/string2.h:1129: error: 'size_t' undeclared (first use in
> this function)
> /usr/include/bits/string2.h:1129: error: expected ';' before '__s'
> /usr/include/bits/string2.h: In function '__strpbrk_c3':
> /usr/include/bits/string2.h:1142: error: 'size_t' undeclared (first use in
> this function)
> /usr/include/bits/string2.h:1142: error: expected ';' before '__s'
> In file included from /usr/include/bits/string2.h:1299,
>                  from /usr/include/string.h:417,
>                  from ../libs/sgeobj/config.c:34:
> /usr/include/stdlib.h: At top level:
> /usr/include/stdlib.h:589: error: expected ')' before '__size'
> /usr/include/stdlib.h:591: error: expected ')' before '__nmemb'
> In file included from /usr/include/string.h:417,
>                  from ../libs/sgeobj/config.c:34:
> /usr/include/bits/string2.h:1323: error: expected declaration specifiers or
> '...' before 'size_t'
> In file included from ../libs/sgeobj/config.c:37:
> /usr/include/stdlib.h:140: error: expected '=', ',', ';', 'asm' or
> '__attribute__' before '__ctype_get_mb_cur_max'
> In file included from /usr/include/sys/types.h:133,
>                  from /usr/include/stdlib.h:438,
>                  from ../libs/sgeobj/config.c:37:
> /usr/include/linux/time.h:10: error: expected specifier-qualifier-list
> before 'time_t'
> /usr/include/linux/time.h:16: error: expected specifier-qualifier-list
> before 'time_t'
> In file included from /usr/include/sys/select.h:46,
>                  from /usr/include/sys/types.h:220,
>                  from /usr/include/stdlib.h:438,
>                  from ../libs/sgeobj/config.c:37:
> /usr/include/bits/time.h:70: error: redefinition of 'struct timeval'
> In file included from ../libs/sgeobj/config.c:37:
> /usr/include/stdlib.h:455: error: expected declaration specifiers or '...'
> before 'size_t'
> /usr/include/stdlib.h:485: error: expected declaration specifiers or '...'
> before 'size_t'
> /usr/include/stdlib.h:487: error: nonnull argument with out-of-range operand
> number (argument 1, operand 4)
> /usr/include/stdlib.h:600: error: expected declaration specifiers or '...'
> before 'size_t'
> In file included from /usr/include/stdlib.h:612,
>                  from ../libs/sgeobj/config.c:37:
> /usr/include/alloca.h:33: error: expected ')' before '__size'
> In file included from ../libs/sgeobj/config.c:37:
> /usr/include/stdlib.h:617: error: expected ')' before '__size'
> /usr/include/stdlib.h:622: error: expected declaration specifiers or '...'
> before 'size_t'
> /usr/include/stdlib.h:622: error: expected declaration specifiers or '...'
> before 'size_t'
> /usr/include/stdlib.h:775: error: expected declaration specifiers or '...'
> before 'size_t'
> /usr/include/stdlib.h:775: error: expected declaration specifiers or '...'
> before 'size_t'
> /usr/include/stdlib.h:776: error: nonnull argument with out-of-range operand
> number (argument 1, operand 5)
> /usr/include/stdlib.h:780: error: expected declaration specifiers or '...'
> before 'size_t'
> /usr/include/stdlib.h:780: error: expected declaration specifiers or '...'
> before 'size_t'
> /usr/include/stdlib.h:781: error: nonnull argument with out-of-range operand
> number (argument 1, operand 4)
> /usr/include/stdlib.h:853: error: expected declaration specifiers or '...'
> before 'size_t'
> /usr/include/stdlib.h:856: error: expected declaration specifiers or '...'
> before 'size_t'
> /usr/include/stdlib.h:860: error: expected declaration specifiers or '...'
> before 'size_t'
> /usr/include/stdlib.h:864: error: expected declaration specifiers or '...'
> before 'size_t'
> /usr/include/stdlib.h:873: error: expected declaration specifiers or '...'
> before 'size_t'
> /usr/include/stdlib.h:876: error: expected ')' before '*' token
> /usr/include/stdlib.h:880: error: expected declaration specifiers or '...'
> before 'wchar_t'
> /usr/include/stdlib.h:884: error: expected '=', ',', ';', 'asm' or
> '__attribute__' before 'mbstowcs'
> /usr/include/stdlib.h:887: error: expected '=', ',', ';', 'asm' or
> '__attribute__' before 'wcstombs'
> /usr/include/stdlib.h:950: error: expected declaration specifiers or '...'
> before 'size_t'
> In file included from ../libs/cull/cull_list.h:40,
>                  from ../libs/cull/cull_listP.h:35,
>                  from ../libs/cull/cull.h:36,
>                  from ../libs/sgeobj/config.c:39:
> ../libs/cull/pack.h:101: error: expected specifier-qualifier-list before
> 'size_t'
> In file included from ../libs/cull/cull_what.h:41,
>                  from ../libs/cull/cull.h:39,
>                  from ../libs/sgeobj/config.c:39:
> ../libs/uti/sge_dstring.h:65: error: expected specifier-qualifier-list
> before 'size_t'
> ../libs/uti/sge_dstring.h:71: error: expected declaration specifiers or
> '...' before 'size_t'
> ../libs/uti/sge_dstring.h:90: error: expected '=', ',', ';', 'asm' or
> '__attribute__' before 'sge_dstring_strlen'
> ../libs/uti/sge_dstring.h:92: error: expected '=', ',', ';', 'asm' or
> '__attribute__' before 'sge_dstring_remaining'
> In file included from ../libs/cull/cull.h:46,
>                  from ../libs/sgeobj/config.c:39:
> ../libs/cull/cull_pack.h:58: error: expected declaration specifiers or '...'
> before 'size_t'
> ../libs/cull/cull_pack.h:58: error: expected declaration specifiers or '...'
> before 'size_t'
> ../libs/cull/cull_pack.h:97: error: expected '=', ',', ';', 'asm' or
> '__attribute__' before 'cull_get_list_packsize'
> ../libs/cull/cull_pack.h:98: error: expected '=', ',', ';', 'asm' or
> '__attribute__' before 'cull_get_elem_packsize'
> In file included from ../libs/uti/sge_parse_num_par.h:36,
>                  from ../libs/sgeobj/config.c:40:
> /usr/include/sys/time.h:58: error: redefinition of 'struct timezone'
> /usr/include/sys/time.h:96: error: expected identifier before numeric
> constant
> /usr/include/sys/time.h:110: error: redefinition of 'struct itimerval'
> In file included from ../libs/sgeobj/config.c:44:
> ../libs/uti/sge_string.h:90: error: expected '=', ',', ';', 'asm' or
> '__attribute__' before 'sge_strlcpy'
> ../libs/sgeobj/config.c: In function 'read_config_list':
> ../libs/sgeobj/config.c:112: error: 'size_t' undeclared (first use in this
> function)
> ../libs/sgeobj/config.c:112: error: expected ';' before '__s1_len'
>  ../libs/sgeobj/config.c:112: error: '__s1_len' undeclared (first use in
> this function)
> cc1: warnings being treated as errors
> ../libs/sgeobj/config.c:112: warning: implicit declaration of function
> 'strlen'
> ../libs/sgeobj/config.c:112: warning: incompatible implicit declaration of
> built-in function 'strlen'
> ../libs/sgeobj/config.c:112: error: '__s2_len' undeclared (first use in this
> function)
> ../libs/sgeobj/config.c:112: warning: left-hand operand of comma expression
> has no effect
> ../libs/sgeobj/config.c:112: error: expected expression before 'const'
> ../libs/sgeobj/config.c:112: error: expected expression before 'const'
> ../libs/sgeobj/config.c:112: error: expected expression before 'const'
> ../libs/sgeobj/config.c:112: error: expected expression before 'const'
> ../libs/sgeobj/config.c:112: warning: left-hand operand of comma expression
> has no effect
> ../libs/sgeobj/config.c:112: error: expected expression before 'const'
> ../libs/sgeobj/config.c:112: error: expected expression before 'const'
> ../libs/sgeobj/config.c:112: warning: left-hand operand of comma expression
> has no effect
> ../libs/sgeobj/config.c:112: error: expected expression before 'const'
> ../libs/sgeobj/config.c:112: error: expected expression before 'const'
> ../libs/sgeobj/config.c:112: error: expected expression before 'const'
> ../libs/sgeobj/config.c:112: error: expected expression before 'const'
> ../libs/sgeobj/config.c:112: warning: left-hand operand of comma expression
> has no effect
> ../libs/sgeobj/config.c:112: error: expected expression before 'const'
> ../libs/sgeobj/config.c:112: error: expected expression before 'const'
> ../libs/sgeobj/config.c:137: warning: incompatible implicit declaration of
> built-in function 'strlen'
> ../libs/sgeobj/config.c:148: error: expected ';' before '__s1_len'
> ../libs/sgeobj/config.c:148: warning: incompatible implicit declaration of
> built-in function 'strlen'
> ../libs/sgeobj/config.c:148: warning: left-hand operand of comma expression
> has no effect
> ../libs/sgeobj/config.c:148: error: expected expression before 'const'
> ../libs/sgeobj/config.c:148: error: expected expression before 'const'
> ../libs/sgeobj/config.c:148: error: expected expression before 'const'
> ../libs/sgeobj/config.c:148: error: expected expression before 'const'
> ../libs/sgeobj/config.c:148: warning: left-hand operand of comma expression
> has no effect
> ../libs/sgeobj/config.c:148: error: expected expression before 'const'
> ../libs/sgeobj/config.c:148: error: expected expression before 'const'
> ../libs/sgeobj/config.c:148: warning: left-hand operand of comma expression
> has no effect
> ../libs/sgeobj/config.c:148: error: expected expression before 'const'
> ../libs/sgeobj/config.c:148: error: expected expression before 'const'
> ../libs/sgeobj/config.c:148: error: expected expression before 'const'
> ../libs/sgeobj/config.c:148: error: expected expression before 'const'
> ../libs/sgeobj/config.c:148: warning: left-hand operand of comma expression
> has no effect
> ../libs/sgeobj/config.c:148: error: expected expression before 'const'
> ../libs/sgeobj/config.c:148: error: expected expression before 'const'
> ../libs/sgeobj/config.c: In function 'set_conf_double':
> ../libs/sgeobj/config.c:561: error: too many arguments to function
> 'strncasecmp'
> make: *** [config.o] Error 1
> not done
>
>
> --
> --tmac
>
> RedHat Certified Engineer #804006984323821 (RHEL4)
> RedHat Certified Engineer #805007643429572 (RHEL5)
>
> Principal Consultant, RABA Technologies
> 240-373-3926 (office) 301-688-4705 (Lab)
>            214-279-3926 (eFAX)
>

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