[mira_talk] can not install mira on cluster computer with suse 10
- From: "wangminixiao" <wangminxiao@xxxxxxxxxx>
- To: <mira_talk@xxxxxxxxxxxxx>
- Date: Fri, 17 Feb 2012 17:12:08 +0800
I’m trying to compile mira 3.4.1 on a cluster computer with suse 10 Linux
system. We’ve upgraded boost and flex to the latest version before
compiling. Since I do not have the administrator authority, necessary libs
were installed under $Home/software.
The locations of the newly-installed libs were informed using option
switches as listed below: “./configure
--prefix=/public/home/zhaozengfang/software/mira
--with-boost=/public/home/zhaozengfang/software/boost148/
--with-boost-libdir=/public/home/zhaozengfang/software/boost148/lib/
--with-tcmalloc-dir=/public/home/zhaozengfang/software/gperf/lib
--enable-64=yes --enable-mirastatic”. It seems OK for this step说明:
http://seqanswers.com/forums/images/smilies/smile.gif. The system reported
that everything looks good.
However, during make step, several errors occurred.说明:
http://seqanswers.com/forums/images/smilies/confused.gif I failed to install
mira on the cluster computer. The last few lines of the error message were
given:
##########################
g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\"
-DPACKAGE_VERSION=\"3.4.0.1\" -DPACKAGE_STRING=\"mira\ 3.4.0.1\"
-DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\"
-DVERSION=\"3.4.0.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1
-DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1
-DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1
-DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1
-DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict
-DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1
-DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1
-DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_NAMESPACES=/\*\*/ -DHAVE_STD=/\*\*/
-DHAVE_STL=/\*\*/ -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/
-DHAVE_BOOST_REGEX=/\*\*/ -DDEVELOPMENTVERSION=0 -DBOUNDTRACKFLAG=1
-DBUGTRACKFLAG=1 -I. -I../../src -DPUBLICQUIET -DAJ_Linux64
-I/public/home/zhaozengfang/software/mira/include -O3 -funroll-loops
-I/public/home/zhaozengfang/software/expat/include -pthread
-I/public/home/zhaozengfang/software/boost148//include -MT exp_flexer.o -MD
-MP -MF .deps/exp_flexer.Tpo -c -o exp_flexer.o exp_flexer.cc
exp_flexer.cc:325:25: error: no ?.nt EXPFlexLexer::yywrap()?.member function
declared in class ?.XPFlexLexer?
exp_flexer.cc: In member function ?.irtual int EXPFlexLexer::yylex()?.
exp_flexer.cc:1313:19: error: ?.ywrap?.was not declared in this scope
exp_flexer.cc: In member function ?.nt EXPFlexLexer::yyinput()?.
exp_flexer.cc:1732:20: error: ?.ywrap?.was not declared in this scope
make[2]: *** [exp_flexer.o] Error 1
make[2]: Leaving directory
`/public/home/zhaozengfang/software/mira-3.4.0.1/src/io'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory
`/public/home/zhaozengfang/software/mira-3.4.0.1/src'
make: *** [all-recursive] Error 1
###########################
There may be something wrong for flex. I’ve tried my best to fix the
problem including add the new libs into environmental variables, but still
failed说明: http://seqanswers.com/forums/images/smilies/mad.gif.
The config.log are ready, I will email it to you if needed. I’m grateful if
you can give me some help.
By the way, how to activate MPI mode in Mira. I’d like to use 20 cpus for
assembling as my dataset is really huge.
Thanks a lot!
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