[GE users] Linux SPARC install problems

rayson rayrayson at gmail.com
Mon Mar 30 16:25:47 BST 2009


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Check your Java installation, make sure that the Java class path and
Java home ($JAVA_HOME) are setup correctly.

If you don't have java installed, a quick fix is to add aimk flags:
-no-java -no-jni

Rayson



On 3/26/09, wdowling <will.dowling at nuim.ie> wrote:
> Hi everyone,
> I'm new to this list so I hope I'm following correct etiquette. I have
> several SPARC workstations and server I would like to install GridEngine
> on. I have Ubuntu 8.10 (Intrepid) installed and things seem to be going
> smoothly. I downloaded the CVS source and aside from a couple problems I
> managed to get to the 'aimk -only-core' stage. This is where it
> generates the following errors:
>
> will at ncg002:~/gridengine/source$ ./aimk -only-core
> Building in directory: /home/will/gridengine/source
> making in LINUXSPARC_26/ for LINUXSPARC at host ncg002
> _________C_O_R_E__S_Y_S_T_E_M_____________
> gcc -O3 -Wall -Werror -Wstrict-prototypes -DUSE_POLL -DLINUX
> -DLINUXSPARC -DLINUXSPARC_26 -D_GNU_SOURCE -DGETHOSTBYNAME_R6
> -DGETHOSTBYADDR_R8 -DLOAD_OPENSSL
> -I/off_home/gridengine/db-4.4.20/lx26-sparc/include/
> -DSGE_ARCH_STRING=lx26-sparc -DTARGET_32BIT -DSPOOLING_dynamic -DSECURE
> -I/off_home/gridengine/openssl-0.9.8h-origin/lx26-sparc/include
> -Wno-strict-aliasing -D_FILE_OFFSET_BITS=64
> -D__SGE_COMPILE_WITH_GETTEXT__
> -I/home/will/gridengine/source/3rdparty/gettext/LINUXSPARC/include
> -D__SGE_NO_USERMAPPING__ -I../common -I../libs -I../libs/uti
> -I../libs/juti -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/stdio.h:75,
> from ../libs/sgeobj/config.c:33:
> /usr/include/libio.h:332: error: expected specifier-qualifier-list
> before ?size_t?
> /usr/include/libio.h:364: error: expected declaration specifiers or
> ?...? before ?size_t?
> /usr/include/libio.h:373: error: expected declaration specifiers or
> ?...? before ?size_t?
> /usr/include/libio.h:493: error: expected ?=?, ?,?, ?;?, ?asm? or
> ?__attribute__? before ?_IO_sgetn?
> In file included from ../libs/sgeobj/config.c:33:
> /usr/include/stdio.h:294: error: expected declaration specifiers or
> ?...? before ?size_t?
> /usr/include/stdio.h:300: error: expected declaration specifiers or
> ?...? before ?size_t?
> /usr/include/stdio.h:312: error: expected declaration specifiers or
> ?...? before ?size_t?
> /usr/include/stdio.h:319: error: expected declaration specifiers or
> ?...? before ?size_t?
> /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:365: error: expected declaration specifiers or
> ?...? before ?size_t?
> /usr/include/stdio.h:367: error: format string argument not a string type
> /usr/include/stdio.h:635: error: expected declaration specifiers or
> ?...? before ?size_t?
> /usr/include/stdio.h:638: error: expected declaration specifiers or
> ?...? before ?size_t?
> /usr/include/stdio.h:648: error: expected declaration specifiers or
> ?...? before ?size_t?
> /usr/include/stdio.h:678: error: expected ?=?, ?,?, ?;?, ?asm? or
> ?__attribute__? before ?fread?
> /usr/include/stdio.h:684: error: expected ?=?, ?,?, ?;?, ?asm? or
> ?__attribute__? before ?fwrite?
> /usr/include/stdio.h:706: error: expected ?=?, ?,?, ?;?, ?asm? or
> ?__attribute__? before ?fread_unlocked?
> /usr/include/stdio.h:708: error: expected ?=?, ?,?, ?;?, ?asm? or
> ?__attribute__? before ?fwrite_unlocked?
> In file included from /usr/include/stdio.h:903,
> from ../libs/sgeobj/config.c:33:
> /usr/include/bits/stdio.h:116: error: expected declaration specifiers or
> ?...? before ?size_t?
> /usr/include/bits/stdio.h: In function ?getline?:
> /usr/include/bits/stdio.h:118: error: ?__n? undeclared (first use in
> this function)
> /usr/include/bits/stdio.h:118: error: (Each undeclared identifier is
> reported only once
> /usr/include/bits/stdio.h:118: error: for each function it appears in.)
> /usr/include/bits/stdio.h:118: error: too many arguments to function
> ?__getdelim?
> In file included from ../libs/sgeobj/config.c:35:
> /usr/include/strings.h: At top level:
> /usr/include/strings.h:34: error: expected declaration specifiers or
> ?...? before ?size_t?
> /usr/include/strings.h:38: error: expected declaration specifiers or
> ?...? before ?size_t?
> /usr/include/strings.h:41: error: expected declaration specifiers or
> ?...? before ?size_t?
> /usr/include/strings.h:58: 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:320,
> 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:320,
> 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:337: error: expected declaration specifiers or
> ?...? before ?size_t?
> /usr/include/stdlib.h:367: error: expected declaration specifiers or
> ?...? before ?size_t?
> /usr/include/stdlib.h:369: error: nonnull argument with out-of-range
> operand number (argument 1, operand 4)
> /usr/include/stdlib.h:471: error: expected ?)? before ?__size?
> /usr/include/stdlib.h:473: error: expected ?)? before ?__nmemb?
> /usr/include/stdlib.h:485: error: expected declaration specifiers or
> ?...? before ?size_t?
> In file included from /usr/include/stdlib.h:497,
> 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:502: error: expected ?)? before ?__size?
> /usr/include/stdlib.h:507: error: expected declaration specifiers or
> ?...? before ?size_t?
> /usr/include/stdlib.h:507: error: expected declaration specifiers or
> ?...? before ?size_t?
> /usr/include/stdlib.h:684: error: expected declaration specifiers or
> ?...? before ?size_t?
> /usr/include/stdlib.h:684: error: expected declaration specifiers or
> ?...? before ?size_t?
> /usr/include/stdlib.h:685: error: nonnull argument with out-of-range
> operand number (argument 1, operand 5)
> /usr/include/stdlib.h:689: error: expected declaration specifiers or
> ?...? before ?size_t?
> /usr/include/stdlib.h:689: error: expected declaration specifiers or
> ?...? before ?size_t?
> /usr/include/stdlib.h:690: error: nonnull argument with out-of-range
> operand number (argument 1, operand 4)
> /usr/include/stdlib.h:692: error: expected declaration specifiers or
> ?...? before ?size_t?
> /usr/include/stdlib.h:692: error: expected declaration specifiers or
> ?...? before ?size_t?
> /usr/include/stdlib.h:694: error: nonnull argument with out-of-range
> operand number (argument 1, operand 4)
> /usr/include/stdlib.h:767: error: expected declaration specifiers or
> ?...? before ?size_t?
> /usr/include/stdlib.h:770: error: expected declaration specifiers or
> ?...? before ?size_t?
> /usr/include/stdlib.h:774: error: expected declaration specifiers or
> ?...? before ?size_t?
> /usr/include/stdlib.h:778: error: expected declaration specifiers or
> ?...? before ?size_t?
> /usr/include/stdlib.h:787: error: expected declaration specifiers or
> ?...? before ?size_t?
> /usr/include/stdlib.h:790: error: expected ?)? before ?*? token
> /usr/include/stdlib.h:794: error: expected declaration specifiers or
> ?...? before ?wchar_t?
> /usr/include/stdlib.h:798: error: expected ?=?, ?,?, ?;?, ?asm? or
> ?__attribute__? before ?mbstowcs?
> /usr/include/stdlib.h:801: error: expected ?=?, ?,?, ?;?, ?asm? or
> ?__attribute__? before ?wcstombs?
> /usr/include/stdlib.h:864: error: expected declaration specifiers or
> ?...? before ?size_t?
> In file included from ../libs/cull/cull_list.h:42,
> from ../libs/cull/cull_listP.h:35,
> from ../libs/cull/cull.h:37,
> 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_list.h:43,
> from ../libs/cull/cull_listP.h:35,
> from ../libs/cull/cull.h:37,
> from ../libs/sgeobj/config.c:39:
> ../libs/uti/sge_dstring.h:66: error: expected specifier-qualifier-list
> before ?size_t?
> ../libs/uti/sge_dstring.h:72: error: expected declaration specifiers or
> ?...? before ?size_t?
> ../libs/uti/sge_dstring.h:77: error: expected declaration specifiers or
> ?...? before ?time_t?
> ../libs/uti/sge_dstring.h:93: error: expected ?=?, ?,?, ?;?, ?asm? or
> ?__attribute__? before ?sge_dstring_strlen?
> ../libs/uti/sge_dstring.h:95: error: expected ?=?, ?,?, ?;?, ?asm? or
> ?__attribute__? before ?sge_dstring_remaining?
> In file included from ../libs/cull/cull.h:47,
> 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?
> 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 /usr/include/asm/signal.h:7,
> from /usr/include/linux/signal.h:4,
> from /usr/include/pthread.h:29,
> from ../libs/comm/lists/cl_lists.h:39,
> from ../libs/comm/cl_commlib.h:39,
> from ../libs/rmon/rmon.h:39,
> from ../libs/rmon/sgermon.h:38,
> from ../libs/sgeobj/config.c:41:
> /usr/include/asm-sparc/signal.h:102: error: conflicting types for ?sigset_t?
> /usr/include/sys/select.h:38: error: previous declaration of ?sigset_t?
> was here
> In file included from /usr/include/asm-sparc/siginfo.h:11,
> from /usr/include/asm/siginfo.h:7,
> from /usr/include/linux/signal.h:5,
> from /usr/include/pthread.h:29,
> from ../libs/comm/lists/cl_lists.h:39,
> from ../libs/comm/cl_commlib.h:39,
> from ../libs/rmon/rmon.h:39,
> from ../libs/rmon/sgermon.h:38,
> from ../libs/sgeobj/config.c:41:
> /usr/include/asm-generic/siginfo.h:55: error: expected
> specifier-qualifier-list before ?timer_t?
> /usr/include/asm-generic/siginfo.h:74: error: expected
> specifier-qualifier-list before ?clock_t?
> In file included from ../libs/comm/lists/cl_lists.h:39,
> from ../libs/comm/cl_commlib.h:39,
> from ../libs/rmon/rmon.h:39,
> from ../libs/rmon/sgermon.h:38,
> from ../libs/sgeobj/config.c:41:
> /usr/include/pthread.h:297: error: expected declaration specifiers or
> ?...? before ?size_t?
> /usr/include/pthread.h:298: error: nonnull argument with out-of-range
> operand number (argument 1, operand 2)
> /usr/include/pthread.h:302: error: expected declaration specifiers or
> ?...? before ?size_t?
> /usr/include/pthread.h:361: error: expected declaration specifiers or
> ?...? before ?size_t?
> /usr/include/pthread.h:362: error: nonnull argument with out-of-range
> operand number (argument 1, operand 2)
> /usr/include/pthread.h:368: error: expected declaration specifiers or
> ?...? before ?size_t?
> /usr/include/pthread.h:375: error: expected declaration specifiers or
> ?...? before ?size_t?
> /usr/include/pthread.h:376: error: nonnull argument with out-of-range
> operand number (argument 1, operand 3)
> /usr/include/pthread.h:382: error: expected declaration specifiers or
> ?...? before ?size_t?
> /usr/include/pthread.h:389: error: expected declaration specifiers or
> ?...? before ?size_t?
> /usr/include/pthread.h:390: error: expected ?;?, ?,? or ?)? before ?*? token
> /usr/include/pthread.h:396: error: expected declaration specifiers or
> ?...? before ?size_t?
> /usr/include/pthread.h:397: error: expected declaration specifiers or
> ?...? before ?cpu_set_t?
> /usr/include/pthread.h:398: error: nonnull argument with out-of-range
> operand number (argument 1, operand 3)
> /usr/include/pthread.h:446: error: expected declaration specifiers or
> ?...? before ?size_t?
> /usr/include/pthread.h:447: error: expected ?;?, ?,? or ?)? before ?*? token
> /usr/include/pthread.h:451: error: expected declaration specifiers or
> ?...? before ?size_t?
> /usr/include/pthread.h:452: error: expected declaration specifiers or
> ?...? before ?cpu_set_t?
> /usr/include/pthread.h:453: error: nonnull argument with out-of-range
> operand number (argument 1, operand 3)
> In file included from /usr/include/sys/uio.h:29,
> from /usr/include/sys/socket.h:28,
> from /usr/include/netinet/in.h:25,
> from /usr/include/arpa/inet.h:23,
> from ../libs/comm/cl_xml_parsing.h:36,
> from ../libs/comm/cl_data_types.h:42,
> from ../libs/comm/cl_commlib.h:40,
> from ../libs/rmon/rmon.h:39,
> from ../libs/rmon/sgermon.h:38,
> from ../libs/sgeobj/config.c:41:
> /usr/include/bits/uio.h:47: error: expected specifier-qualifier-list
> before ?size_t?
> In file included from /usr/include/sys/socket.h:36,
> from /usr/include/netinet/in.h:25,
> from /usr/include/arpa/inet.h:23,
> from ../libs/comm/cl_xml_parsing.h:36,
> from ../libs/comm/cl_data_types.h:42,
> from ../libs/comm/cl_commlib.h:40,
> from ../libs/rmon/rmon.h:39,
> from ../libs/rmon/sgermon.h:38,
> from ../libs/sgeobj/config.c:41:
> /usr/include/bits/socket.h:225: error: expected specifier-qualifier-list
> before ?size_t?
> /usr/include/bits/socket.h:239: error: expected specifier-qualifier-list
> before ?size_t?
> /usr/include/bits/socket.h: In function ?__cmsg_nxthdr?:
> /usr/include/bits/socket.h:276: error: ?size_t? undeclared (first use in
> this function)
> /usr/include/bits/socket.h:276: error: expected ?)? before ?__cmsg?
> /usr/include/bits/socket.h:281: error: ?struct cmsghdr? has no member
> named ?cmsg_len?
> /usr/include/bits/socket.h:281: error: expected ?)? before ?~? token
> /usr/include/bits/socket.h:282: error: ?struct msghdr? has no member
> named ?msg_control?
> /usr/include/bits/socket.h:283: error: ?struct msghdr? has no member
> named ?msg_controllen?
> /usr/include/bits/socket.h:284: error: ?struct cmsghdr? has no member
> named ?cmsg_len?
> /usr/include/bits/socket.h:284: error: expected ?)? before ?~? token
> /usr/include/bits/socket.h:285: error: ?struct msghdr? has no member
> named ?msg_control?
> /usr/include/bits/socket.h:285: error: ?struct msghdr? has no member
> named ?msg_controllen?
> In file included from /usr/include/netinet/in.h:25,
> from /usr/include/arpa/inet.h:23,
> from ../libs/comm/cl_xml_parsing.h:36,
> from ../libs/comm/cl_data_types.h:42,
> from ../libs/comm/cl_commlib.h:40,
> from ../libs/rmon/rmon.h:39,
> from ../libs/rmon/sgermon.h:38,
> from ../libs/sgeobj/config.c:41:
> /usr/include/sys/socket.h: At top level:
> /usr/include/sys/socket.h:137: error: expected declaration specifiers or
> ?...? before ?size_t?
> /usr/include/sys/socket.h:144: error: expected declaration specifiers or
> ?...? before ?size_t?
> /usr/include/sys/socket.h:151: error: expected declaration specifiers or
> ?...? before ?size_t?
> /usr/include/sys/socket.h:162: error: expected declaration specifiers or
> ?...? before ?size_t?
> In file included from ../libs/comm/cl_xml_parsing.h:36,
> from ../libs/comm/cl_data_types.h:42,
> from ../libs/comm/cl_commlib.h:40,
> from ../libs/rmon/rmon.h:39,
> from ../libs/rmon/sgermon.h:38,
> from ../libs/sgeobj/config.c:41:
> /usr/include/arpa/inet.h:78: error: expected declaration specifiers or
> ?...? before ?size_t?
> /usr/include/arpa/inet.h:84: error: expected declaration specifiers or
> ?...? before ?size_t?
> /usr/include/arpa/inet.h:90: error: expected declaration specifiers or
> ?...? before ?size_t?
> In file included from ../libs/sgeobj/config.c:44:
> ../libs/uti/sge_string.h:94: error: expected ?=?, ?,?, ?;?, ?asm? or
> ?__attribute__? before ?sge_strlcpy?
> cc1: warnings being treated as errors
> ../libs/sgeobj/config.c: In function ?read_config_list?:
> ../libs/sgeobj/config.c:112: warning: implicit declaration of function
> ?strcmp?
> ../libs/sgeobj/config.c:122: warning: implicit declaration of function
> ?strchr?
> ../libs/sgeobj/config.c:122: warning: incompatible implicit declaration
> of built-in function ?strchr?
> ../libs/sgeobj/config.c:137: warning: implicit declaration of function
> ?strlen?
> ../libs/sgeobj/config.c:137: warning: incompatible implicit declaration
> of built-in function ?strlen?
> ../libs/sgeobj/config.c:140: warning: incompatible implicit declaration
> of built-in function ?strchr?
> ../libs/sgeobj/config.c: In function ?get_conf_value?:
> ../libs/sgeobj/config.c:261: warning: implicit declaration of function
> ?strcpy?
> ../libs/sgeobj/config.c:261: warning: incompatible implicit declaration
> of built-in function ?strcpy?
> ../libs/sgeobj/config.c: In function ?set_conf_string?:
> ../libs/sgeobj/config.c:303: warning: incompatible implicit declaration
> of built-in function ?strcpy?
> ../libs/sgeobj/config.c:307: warning: incompatible implicit declaration
> of built-in function ?strcpy?
> ../libs/sgeobj/config.c:311: warning: incompatible implicit declaration
> of built-in function ?strcpy?
> ../libs/sgeobj/config.c: In function ?set_conf_double?:
> ../libs/sgeobj/config.c:561: error: too many arguments to function
> ?strncasecmp?
> ../libs/sgeobj/config.c: In function ?set_conf_list?:
> ../libs/sgeobj/config.c:834: warning: incompatible implicit declaration
> of built-in function ?strcpy?
> ../libs/sgeobj/config.c:838: warning: incompatible implicit declaration
> of built-in function ?strcpy?
> ../libs/sgeobj/config.c:842: warning: incompatible implicit declaration
> of built-in function ?strcpy?
> make: *** [config.o] Error 1
> not done
>
> I have searched around and found a couple people with similar errors but
> no solutions. I have only basic familiarization with C so my guesses are
> scarce. Has anyone got any ideas if this is a SPARC/C library/GridEngine
> source problem?
>
> Thanks,
> Will
>
> --
>
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>
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