问题描述
我正在尝试在服务器节点(而不是服务器登录)上构建dssp(https://github.com/cmbi/dssp),并且我正面临系统如何查找依赖项的问题。我正在使用centos 7。
构建dssp的过程是:run ./autogen
获得configure.sh
文件,然后执行该文件。然后运行make
。
运行whereis perl
和whereis perl5
我得到:
[mavridks@haswell-182 dssp-2.3.0]$ whereis perl
perl: /usr/bin/perl /usr/share/man/man1/perl.1.gz
[mavridks@haswell-182 dssp-2.3.0]$ whereis perl5
perl5: /usr/lib64/perl5 /usr/share/perl5
然后运行./autogen
,我得到了错误:
Can't locate Data/Dumper.pm in @INC
(@INC contains:
/hits/sw/shared/apps/Autoconf/2.69-GCC-4.8.4/share/autoconf
/usr/local/lib64/perl5
/usr/local/share/perl5
/usr/lib64/perl5/vendor_perl
/usr/share/perl5/vendor_perl
/usr/lib64/perl5
/usr/share/perl5
.)
at /hits/sw/shared/apps/Autoconf/2.69-GCC-4.8.4/share/autoconf/Autom4te/C4che.pm line 33.
BEGIN Failed--compilation aborted
at /hits/sw/shared/apps/Autoconf/2.69-GCC-4.8.4/share/autoconf/Autom4te/C4che.pm line 33.
Compilation Failed in require
at /hits/sw/shared/apps/Autoconf/2.69-GCC-4.8.4/bin/autom4te line 37.
BEGIN Failed--compilation aborted
at /hits/sw/shared/apps/Autoconf/2.69-GCC-4.8.4/bin/autom4te line 37.
aclocal: error: echo Failed with exit status: 2
(添加了换行符以提高可读性。)
在我看来,调用autoconf
时出现此错误是与无法正确定位Perl文件或具有比应有的路径更多有关?另一个想法是我在服务器上没有root特权,也许这会引起问题?
欢迎任何想法或建议。
注意: 服务器使用模块系统来加载各种依赖项。我需要自动工具和Boost。我正在使用的模块(如果这很重要)是
[mavridks@haswell-182 dssp-2.3.0]$ module list
Currently Loaded Modules:
1) numactl/.2.0.10-GCC-4.8.4 (H)
2) hwloc/.1.10.1-GCC-4.8.4 (H)
3) OpenMPI/1.8.4-GCC-4.8.4
4) OpenBLAS/0.2.13-GCC-4.8.4-LAPACK-3.5.0
5) gompi/1.7.20
6) FFTW/3.3.4-gompi-1.7.20
7) ScaLAPACK/2.0.2-gompi-1.7.20-OpenBLAS-0.2.13-LAPACK-3.5.0
8) goolf/1.7.20
9) bzip2/.1.0.6-goolf-1.7.20 (H)
10) zlib/.1.2.8-goolf-1.7.20 (H)
11) Boost/1.58.0-goolf-1.7.20
12) slurm/18-08-4-1-hits
13) GCC/4.8.4
14) gcc/dummy
15) sge/dummy
16) M4/1.4.17-GCC-4.8.4
17) Autoconf/2.69-GCC-4.8.4
18) Automake/1.15-GCC-4.8.4
19) libtool/2.4.6-GCC-4.8.4
20) Autotools/20150215-GCC-4.8.4
Where:
H: Hidden Module
编辑:
在HåkonHægland发表评论后,我得到了:
[mavridks@haswell-005 ~]$ perl --version | grep 'This is'
This is perl 5,version 30,subversion 0 (v5.30.0) built for x86_64-linux-thread-multi
[mavridks@haswell-005 ~]$ perl -MData::Dumper -E 'say $INC{"Data/Dumper.pm"}'
/hits/sw/shared/apps/Perl/5.30.0-GCCcore-8.3.0/lib/perl5/5.30.0/x86_64-linux-thread-multi/Data/Dumper.pm
编辑2:
这是重新运行./autogen
[mavridks@haswell-112 dssp-2.3.0]
$ PERL5LIB=/hits/sw/shared/apps/Perl/5.30.0-GCCcore-8.3.0/lib/perl5/5.30.0 ./autogen.sh
/hits/sw/shared/apps/Automake/1.15-GCC-4.8.4/bin/aclocal:
Perl lib version (5.30.0) doesn't match executable '/usr/bin/perl' version (5.16.3)
at /hits/sw/shared/apps/Perl/5.30.0-GCCcore-8.3.0/lib/perl5/5.30.0/x86_64-linux-thread-multi/Config.pm line 62.
Compilation Failed in require
at /hits/sw/shared/apps/Automake/1.15-GCC-4.8.4/share/automake-1.15/Automake/Config.pm line 41.
BEGIN Failed--compilation aborted
at /hits/sw/shared/apps/Automake/1.15-GCC-4.8.4/share/automake-1.15/Automake/Config.pm line 41.
Compilation Failed in require
at /hits/sw/shared/apps/Automake/1.15-GCC-4.8.4/bin/aclocal line 37.
BEGIN Failed--compilation aborted
at /hits/sw/shared/apps/Automake/1.15-GCC-4.8.4/bin/aclocal line 37.
(添加了换行符以提高可读性。)
编辑3:
-
第一个连接到服务器登录节点。运行whereis perl会给出:
[mavridks @ haswell-login〜] $ whereis perl
perl:/ usr / bin / perl /usr/share/man/man1/perl.1.gz
也可以运行
[mavridks@haswell-login ~]$ perl --version
This is perl 5,version 16,subversion 3 (v5.16.3) built for x86_64-
linux-thread-multi
(with 39 registered patches,see perl -V for more detail)
。最后一个得到:
[mavridks@haswell-login ~]$ perl -MData::Dumper -E 'say
$INC{"Data/Dumper.pm"}'
/usr/lib64/perl5/vendor_perl/Data/Dumper.pm
旁注:运行perl -V会得到什么?
a)在登录节点上:
[mavridks@haswell-login ~]$ perl -V
Summary of my perl5 (revision 5 version 16 subversion 3) configuration:
Platform:
osname=linux,osvers=3.10.0-693.17.1.el7.x86_64,archname=x86_64-linux-thread-multi
uname='linux x86-01.bsys.centos.org 3.10.0-693.17.1.el7.x86_64 #1 smp thu jan 25 20:13:58 utc 2018 x86_64 x86_64 x86_64 gnulinux '
config_args='-des -Doptimize=-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -Dccdlflags=-Wl,--enable-new-dtags -Dlddlflags=-shared -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -Wl,-z,relro -DDEBUGGING=-g -Dversion=5.16.3 -Dmyhostname=localhost -Dperladmin=root@localhost -Dcc=gcc -Dcf_by=Red Hat,Inc. -Dprefix=/usr -Dvendorprefix=/usr -Dsiteprefix=/usr/local -Dsitelib=/usr/local/share/perl5 -Dsitearch=/usr/local/lib64/perl5 -Dprivlib=/usr/share/perl5 -Dvendorlib=/usr/share/perl5/vendor_perl -Darchlib=/usr/lib64/perl5 -Dvendorarch=/usr/lib64/perl5/vendor_perl -Darchname=x86_64-linux-thread-multi -Dlibpth=/usr/local/lib64 /lib64 /usr/lib64 -Duseshrplib -Dusethreads -Duseithreads -Dusedtrace=/usr/bin/dtrace -Duselargefiles -Dd_semctl_semun -Di_db -Ui_ndbm -Di_gdbm -Di_shadow -Di_syslog -Dman3ext=3pm -Duseperlio -Dinstallusrbinperl=n -Ubincompat5005 -Uversiononly -Dpager=/usr/bin/less -isr -Dd_gethostent_r_proto -Ud_endhostent_r_proto -Ud_sethostent_r_proto -Ud_endprotoent_r_proto -Ud_setprotoent_r_proto -Ud_endservent_r_proto -Ud_setservent_r_proto -Dscriptdir=/usr/bin -Dusesitecustomize'
hint=recommended,useposix=true,d_sigaction=define
useithreads=define,usemultiplicity=define
useperlio=define,d_sfio=undef,uselargefiles=define,usesocks=undef
use64bitint=define,use64bitall=define,uselongdouble=undef
usemymalloc=n,bincompat5005=undef
Compiler:
cc='gcc',ccflags ='-D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64',optimize='-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic',cppflags='-D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include'
ccversion='',gccversion='4.8.5 20150623 (Red Hat 4.8.5-36)',gccosandvers=''
intsize=4,longsize=8,ptrsize=8,doublesize=8,byteorder=12345678
d_longlong=define,longlongsize=8,d_longdbl=define,longdblsize=16
ivtype='long',ivsize=8,nvtype='double',nvsize=8,Off_t='off_t',lseeksize=8
alignbytes=8,prototype=define
Linker and Libraries:
ld='gcc',ldflags =' -fstack-protector'
libpth=/usr/local/lib64 /lib64 /usr/lib64
libs=-lresolv -lnsl -lgdbm -ldb -ldl -lm -lcrypt -lutil -lpthread -lc -lgdbm_compat
perllibs=-lresolv -lnsl -ldl -lm -lcrypt -lutil -lpthread -lc
libc=,so=so,useshrplib=true,libperl=libperl.so
gnulibc_version='2.17'
Dynamic Linking:
dlsrc=dl_dlopen.xs,dlext=so,d_dlsymun=undef,ccdlflags='-Wl,--enable-new-dtags -Wl,-rpath,/usr/lib64/perl5/CORE'
cccdlflags='-fPIC',lddlflags='-shared -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -Wl,relro '
characteristics of this binary (from libperl):
Compile-time options: HAS_TIMES MULTIPLICITY PERLIO_LAYERS
PERL_DONT_CREATE_GVSV PERL_IMPLICIT_CONTEXT
PERL_MALLOC_WRAP PERL_PRESERVE_IVUV USE_64_BIT_ALL
USE_64_BIT_INT USE_ITHREADS USE_LARGE_FILES
USE_LOCALE USE_LOCALE_COLLATE USE_LOCALE_CTYPE
USE_LOCALE_NUMERIC USE_PERLIO USE_PERL_ATOF
USE_REENTRANT_API USE_SITECUSTOMIZE
Locally applied patches:
Fedora Patch1: Removes date check,Fedora/RHEL specific
Fedora Patch3: support for libdir64
Fedora Patch4: use libresolv instead of libbind
Fedora Patch5: USE_MM_LD_RUN_PATH
Fedora Patch6: Skip hostname tests,due to builders not being network capable
Fedora Patch7: Dont run one io test due to random builder failures
Fedora Patch9: Fix find2perl to translate ? glob properly (RT#113054)
Fedora Patch10: Fix broken atof (RT#109318)
Fedora Patch13: Clear $@ before "do" I/O error (RT#113730)
Fedora Patch14: Do not truncate syscall() return value to 32 bits (RT#113980)
Fedora Patch15: Override the Pod::Simple::parse_file (CPANRT#77530)
Fedora Patch16: Do not leak with attribute on my variable (RT#114764)
Fedora Patch17: Allow operator after numeric keyword argument (RT#105924)
Fedora Patch18: Extend stack in File::Glob::glob,(RT#114984)
Fedora Patch19: Do not crash when vivifying $|
Fedora Patch20: Fix misparsing of maketext strings (CVE-2012-6329)
Fedora Patch21: Add NAME headings to CPAN modules (CPANRT#73396)
Fedora Patch22: Fix leaking tied hashes (RT#107000) [1]
Fedora Patch23: Fix leaking tied hashes (RT#107000) [2]
Fedora Patch24: Fix leaking tied hashes (RT#107000) [3]
Fedora Patch25: Fix dead lock in PerlIO after fork from thread (RT#106212)
Fedora Patch26: Make regexp safe in a signal handler (RT#114878)
Fedora Patch27: Update h2ph(1) documentation (RT#117647)
Fedora Patch28: Update pod2html(1) documentation (RT#117623)
Fedora Patch29: Document Math::BigInt::CalcEmu requires Math::BigInt (CPAN RT#85015)
RHEL Patch30: Use stronger algorithm needed for FIPS in t/op/crypt.t (RT#121591)
RHEL Patch31: Make *DBM_File desctructors thread-safe (RT#61912)
RHEL Patch32: Use stronger algorithm needed for FIPS in t/op/taint.t (RT#123338)
RHEL Patch33: Remove cpu-speed-sensitive test in Benchmark test
RHEL Patch34: Make File::Glob work with threads again
RHEL Patch35: Fix CRLF conversion in ASCII FTP upload (CPAN RT#41642)
RHEL Patch36: Do not leak the temp utf8 copy of namepv (CPAN RT#123786)
RHEL Patch37: Fix duplicating PerlIO::encoding when spawning threads (RT#31923)
RHEL Patch38: Add SSL support to Net::SMTP (CPAN RT#93823) [1]
RHEL Patch39: Add SSL support to Net::SMTP (CPAN RT#93823) [2]
RHEL Patch40: Add SSL support to Net::SMTP (CPAN RT#93823) [3]
RHEL Patch41: Add SSL support to Net::SMTP (CPAN RT#93823) [4]
RHEL Patch42: Do not overload ".." in Math::BigInt (CPAN RT#80182)
RHEL Patch43: Fix CVE-2018-18311 Integer overflow leading to buffer overflow
Built under linux
Compiled at Jan 21 2019 22:09:19
@INC:
/usr/local/lib64/perl5
/usr/local/share/perl5
/usr/lib64/perl5/vendor_perl
/usr/share/perl5/vendor_perl
/usr/lib64/perl5
/usr/share/perl5
.
[mavridks@haswell-login ~]$
b)在gpu节点上:
[mavridks@haswell-179 ~]$ perl -V
Summary of my perl5 (revision 5 version 16 subversion 3) configuration:
Platform:
osname=linux,(RT#114984)
Fedora Patch19: Do not crash when vivifying $|
Fedora Patch20: Fix misparsing of maketext strings (CVE-2012-6329)
Fedora Patch21: Add NAME headings to CPAN modules (CPANRT#73396)
Fedora Patch22: Fix leaking tied hashes (RT#107000) [1]
Fedora Patch23: Fix leaking tied hashes (RT#107000) [2]
Fedora Patch24: Fix leaking tied hashes (RT#107000) [3]
Fedora Patch25: Fix dead lock in PerlIO after fork from thread (RT#106212)
Fedora Patch26: Make regexp safe in a signal handler (RT#114878)
Fedora Patch27: Update h2ph(1) documentation (RT#117647)
Fedora Patch28: Update pod2html(1) documentation (RT#117623)
Fedora Patch29: Document Math::BigInt::CalcEmu requires Math::BigInt (CPAN RT#85015)
RHEL Patch30: Use stronger algorithm needed for FIPS in t/op/crypt.t (RT#121591)
RHEL Patch31: Make *DBM_File desctructors thread-safe (RT#61912)
RHEL Patch32: Use stronger algorithm needed for FIPS in t/op/taint.t (RT#123338)
RHEL Patch33: Remove cpu-speed-sensitive test in Benchmark test
RHEL Patch34: Make File::Glob work with threads again
RHEL Patch35: Fix CRLF conversion in ASCII FTP upload (CPAN RT#41642)
RHEL Patch36: Do not leak the temp utf8 copy of namepv (CPAN RT#123786)
RHEL Patch37: Fix duplicating PerlIO::encoding when spawning threads (RT#31923)
RHEL Patch38: Add SSL support to Net::SMTP (CPAN RT#93823) [1]
RHEL Patch39: Add SSL support to Net::SMTP (CPAN RT#93823) [2]
RHEL Patch40: Add SSL support to Net::SMTP (CPAN RT#93823) [3]
RHEL Patch41: Add SSL support to Net::SMTP (CPAN RT#93823) [4]
RHEL Patch42: Do not overload ".." in Math::BigInt (CPAN RT#80182)
Built under linux
Compiled at Oct 30 2018 18:59:43
@INC:
/usr/local/lib64/perl5
/usr/local/share/perl5
/usr/lib64/perl5/vendor_perl
/usr/share/perl5/vendor_perl
/usr/lib64/perl5
/usr/share/perl5
.
-
然后连接到一个gpu节点。看来我们仍然有相同的perl:
[mavridks @ haswell-179〜] $ whereis perl perl:/ usr / bin / perl /usr/share/man/man1/perl.1.gz
但是现在Data / Dumber不再可用了(运行perl -MData :: Dumper -E'say $ INC {“ Data / Dumper.pm”}')):
[mavridks@haswell-179 ~]$ perl -MData::Dumper -E 'say $INC{"Data/Dumper.pm"}'
Can't locate Data/Dumper.pm in @INC (@INC contains: /usr/local/lib64/perl5 /usr/local/share/perl5 /usr/lib64/perl5/vendor_perl /usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5 .).
BEGIN Failed--compilation aborted.
-
然后,IT部门建议加载perl模块。服务器建立在模块系统上,其中所有组都可以将软件作为模块加载(在路径中附加正确的文件-这是https://lmod.readthedocs.io/en/latest/#overview使用的系统)。因此,如果我们运行模块加载Perl,我们将:
[mavridks @ haswell-179〜] $ whereis perl perl:/ usr / bin / perl /hits/sw/shared/apps/Perl/5.30.0-GCCcore-8.3.0/bin/perl /usr/share/man/man1/perl.1.gz
这意味着我们已经更改了某些内容(我可以说使用的分布是什么?)。但是现在我们有了:
[mavridks@haswell-179 ~]$ perl -MData::Dumper -E 'say $INC{"Data/Dumper.pm"}'
/hits/sw/shared/apps/Perl/5.30.0-GCCcore-8.3.0/lib/perl5/5.30.0/x86_64-linux-thread-multi/Data/Dumper.pm
这意味着我们在系统上有数据/转储器。
-
最后,还需要将所有自动工具作为模块加载。然后,似乎autogen.sh脚本的执行是在系统中寻找perl模块(一个来自login而不是gpu的模块),但是当然找不到它们。
[mavridks @ haswell-179 dssp-2.3.0] $ ./autogen.sh 无法在@INC中找到Data / Dumper.pm(@INC包含:/hits/sw/shared/apps/Autoconf/2.69-GCC-4.8.4/share/autoconf / usr / local / lib64 / perl5 / usr /本地/共享/ perl5 / usr / lib64 / perl5 / vendor_perl / usr / share / perl5 / vendor_perl / usr / lib64 / perl5 / usr / share / perl5。)在/hits/sw/shared/apps/Autoconf/2.69-GCC -4.8.4 / share / autoconf / Autom4te / C4che.pm第33行。 BEGIN失败-在/hits/sw/shared/apps/Autoconf/2.69-GCC-4.8.4/share/autoconf/Autom4te/C4che.pm第33行中,编译中止。 在/hits/sw/shared/apps/Autoconf/2.69-GCC-4.8.4/bin/autom4te第37行,要求中的编译失败。 BEGIN失败-编译在/hits/sw/shared/apps/Autoconf/2.69-GCC-4.8.4/bin/autom4te第37行中止。 aclocal:错误:回显失败,退出状态:2
解决方法
您已经安装了两个perl
版本。
-
/usr/bin/perl
,v5.16.3 [1] -
/hits/sw/shared/apps/Perl/5.30.0-GCCcore-8.3.0/bin/perl
,v5.30.0 [2]
我将分别命名为“系统perl
”和“模块化perl
”。
- 系统
perl
未安装Data :: Dumper。 [3] - 模块化
perl
确实安装了Data :: Dumper。 [4]
whereis
在您的PATH中仅显示系统perl
,但以后的命令显示perl
调用模块化perl
。因此,perl
是模块化perl
的别名, [5] ,或者您在不同的环境中运行测试(即,更改了PATH)。
设置PERL5LIB
是否合适?
有一次,您将环境变量PERL5LIB
设置为/hits/sw/shared/apps/Perl/5.30.0-GCCcore-8.3.0/lib/perl5/5.30.0
。这不合适。
这对于系统perl
是不正确的。 [6]
对于模块化perl
,这是不必要的。这是多余的。 [7]
为什么系统perl
上没有安装Data :: Dumper?
Perl随附某些模块。实际上,只要Perl中一直存在对模块的支持,就包括Data :: Dumper。 Data :: Dumper应该始终可用。
但是,某些Linux发行版将Perl分为多个软件包。似乎在CentOS 7的perl(Data::Dumper)
package中找到了Data :: Dumper。
因此解决方案是安装该软件包。
由于Data :: Dumper具有双重作用,因此也可以从CPAN安装它。这不需要任何特殊权限。也就是说,我通常建议在本地安装perl
而不是弄乱系统perl
。看来您已经有了这样的Perl。这会将我们引向下一个子答案。
我要使用模块化的perl
怎么办?
我不确定。
快速实验使我相信,只需将模块化perl
放在/usr/bin
之前的PATH中即可解决。
export PATH="/hits/sw/shared/apps/Perl/5.30.0-GCCcore-8.3.0/bin:$PATH"
或者,快速实验表明以下两种方法也可以工作:
./configure PERL=/hits/sw/shared/apps/Perl/5.30.0-GCCcore-8.3.0/bin/perl
PERL=/hits/sw/shared/apps/Perl/5.30.0-GCCcore-8.3.0/bin/perl ./configure
如果这些方法不能解决问题,可以将其作为一个单独的问题进行询问。
如果我不同意此答案中的某些内容怎么办?
我的某些陈述是猜测。例如,问题中的任何地方都没有提到/hits/sw/shared/apps/Perl/5.30.0-GCCcore-8.3.0/bin/perl
。如果您认为我做错了,请提供以下命令的输出(parens和全部):
(
echo 'System perl:'
/usr/bin/perl -v | grep 'This is'
PERL5LIB= /usr/bin/perl -e'CORE::say for @INC'
echo
echo "Data::Dumper in system perl?"
PERL5LIB= /usr/bin/perl -e'
use Data::Dumper;
CORE::say $Data::Dumper::VERSION;
CORE::say INC{"Data/Dumper.pm"};
'
echo
echo 'Modular perl:'
/hits/sw/shared/apps/Perl/5.30.0-GCCcore-8.3.0/bin/perl -v | grep 'This is'
PERL5LIB= /hits/sw/shared/apps/Perl/5.30.0-GCCcore-8.3.0/bin/perl -e'CORE::say for @INC'
echo
echo "Data::Dumper in modular perl?"
PERL5LIB= /hits/sw/shared/apps/Perl/5.30.0-GCCcore-8.3.0/bin/perl -e'
use Data::Dumper;
CORE::say $Data::Dumper::VERSION;
CORE::say $INC{"Data/Dumper.pm"};
'
echo
echo 'Perl env vars:'
perl -e'CORE::say "$_: $ENV{$_}" for grep /^PERL/,keys(%ENV)'
echo
echo 'type perl:'
type perl
)
脚注。
-
可以使用
进行验证/usr/bin/perl -v | grep 'This is'
-
可以使用
进行验证/hits/sw/shared/apps/Perl/5.30.0-GCCcore-8.3.0/bin/perl -v | grep 'This is'
-
可以使用
进行验证/usr/bin/perl -e'use Data::Dumper;'
-
可以使用
进行验证/hits/sw/shared/apps/Perl/5.30.0-GCCcore-8.3.0/bin/perl -e'use Data::Dumper;'
-
在某些shell中(包括
进行验证dash
,bash
和ksh
),可以使用type perl
-
这就是导致
Perl lib version (5.30.0) doesn't match executable '/usr/bin/perl' version (5.16.3)
的原因。 -
可以使用
进行验证PERL5LIB= /hits/sw/shared/apps/Perl/5.30.0-GCCcore-8.3.0/bin/perl -e'CORE::say for @INC;'