Error during Installation on qbc and qb

[enikidis]

CC ttime.o
CC tunicode.o
CC tvlstr.o
CC tvltypes.o
CCLD testhdf5
ld: warning: libimf.so, needed by ../src/.libs/libhdf5.so, not found (try using -rpath or -rpath-link)
ld: warning: libsvml.so, needed by ../src/.libs/libhdf5.so, not found (try using -rpath or -rpath-link)
ld: warning: libirng.so, needed by ../src/.libs/libhdf5.so, not found (try using -rpath or -rpath-link)
ld: warning: libintlc.so.5, needed by ../src/.libs/libhdf5.so, not found (try using -rpath or -rpath-link)
ld: .libs/testhdf5: hidden symbol __intel_cpu_features_init_x' in /usr/local/compilers/Intel/parallel_studio_xe_2019.5/compilers_and_libraries/linux/lib/intel64//libirc.a(cpu_feature_disp.o) is referenced by DSO ld: final link failed: Bad value make[1]: *** [testhdf5] Error 1 make[1]: Leaving directory /tmp/enikidis-asgs/hdf5-1.12.2/test'
make: *** [install-recursive] Error 1
something went wrong with HD5
command for "Step for HDF5 libraries and utilities" exited with an error code of 1, stopping. Please fix and rerun.

./update-asgs --clean Didn't solve the problem in either machine.

[wwlwpd]

this is happening on qbc and qb2?

[wwlwpd]

anywhere else that you know of?

[jasonfleming]

I've installed on both these machines within the past couple days ... I wonder if it was a transient issue with the intel compiler. Remember that time we were getting strange intermittent build failures and it was because they didn't have enough intel compiler licenses?

[wwlwpd]

intel compiler licenses...

I do remember that, have not run into it in a long time.

[enikidis]

Update:
This is just an observation, I am just mentioning it to just help. When I was installing asgs on supermic I used tmux to close my instance session and let it install. For qbc and qb on my previous tries I used screen as you suggested.

Apparently this error disapears if I start my installation outside screen.
Currently I have succesfully built asgs on qbc and installing adcirc. And for qb I passed the point this error previously appeared!

So we have success here !

[enikidis]

Correlation does not imply causation so don't take my comment for screen 100% for granted :)

[jasonfleming]

here is a workaround for this issue : in ~/.bash_profile add the line

export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/compilers/Intel/parallel_studio_xe_2019.5/compilers_and_libraries/linux/lib/intel64

[wwlwpd]

What does your ~/.modules file look like @enikidis ?

Mine looks like this,

module load intel/19.0.5
module load mvapich2/2.3.3/intel-19.0.5

Please try that before you set LD_* flags - this is a recipe for breakage later because you'll forget about it as some point and won't discover it until after a bit of time messing around with it.

[enikidis]

Ok thanks @jasonfleming @wwlwpd the next time there is a need for me to reinstall I will try both of these. Thanks a lot.

Currently I don't want to touch my installations :)

[wwlwpd]

working on reproducing this

[wwlwpd]

I am unable to reproduce this on QBC, working on QB2

[wwlwpd]

I've installed on both these machines within the past couple days ... I wonder if it was a transient issue with the intel compiler. Remember that time we were getting strange intermittent build failures and it was because they didn't have enough intel compiler licenses?

I had a weird issue with the perl install failing on QBC and ls6 at the same time, but it seemed to be that the CPAN Perl mirrors had a hiccup. I re-ran both with no issue.

I am 95% there's an issue with @enikidis' environment so we need to get the env dump for both inside and outside of tmux. This will expose the issue.

[wwlwpd]

Can also not reproduce on qb2. @enikidis please provide the 2 different dumps of env (inside and outside of tmux) so we can see what's going on with your environment.

[jasonfleming]

@wwlwpd I have just reproduced this exact issue. I am running the installation inside screen. I did the env dumps and then ran a diff on them as follows:

# inside screen session
$ env > ~/screen.env
# outside screen session 
$ env > ~/login.env
$ diff --ignore-space-change ~/login.env ~/screen.env > env.diff

It looks like there are differences in the LD_LIBRARY_PATH at least:

4d3
< PKG_CONFIG_PATH_modshare=/usr/local/packages/mvapich2/2.3.3/axaxsfxv/lib/pkgconfig:1
5a5
> PKG_CONFIG_PATH_modshare=/usr/local/packages/mvapich2/2.3.3/axaxsfxv/lib/pkgconfig:1
6a7
> INTEL_LICENSE_FILE=/usr/local/compilers/Intel
8d8
< INTEL_LICENSE_FILE=/usr/local/compilers/Intel/
10d9
< TERM=xterm-256color
11a11
> TERM=screen
14d13
< LIBRARY_PATH_modshare=/usr/local/compilers/Intel/parallel_studio_xe_2019.5/compilers_and_libraries/linux/lib/intel64/:1:/usr/local/compilers/Intel/parallel_studio_xe_2019.5/mkl/lib/intel64:1:/usr/local/packages/mvapich2/2.3.3/axaxsfxv/lib:1
16c15,16
< QTDIR=/usr/lib64/qt-3.3
---
> LIBRARY_PATH_modshare=/usr/local/compilers/Intel/parallel_studio_xe_2019.5/compilers_and_libraries/linux/lib/intel64/:1:/usr/local/compilers/Intel/parallel_studio_xe_2019.5/mkl/lib/intel64:1:/usr/local/packages/mvapich2/2.3.3/axaxsfxv/lib:1
> OLDPWD=/work/jgflemin/production
18,19c18
< QTINC=/usr/lib64/qt-3.3/include
< LANGUAGE_TERRITORY=en_US
---
> QTDIR=/usr/lib64/qt-3.3
21c20,21
< MIC_LD_LIBRARY_PATH=/usr/local/compilers/Intel/parallel_studio_xe_2019.5/compiler/lib/mic:/usr/local/compilers/Intel/parallel_studio_xe_2019.5/mkl/lib/mic
---
> LANGUAGE_TERRITORY=en_US
> QTINC=/usr/lib64/qt-3.3/include
22a23
> MIC_LD_LIBRARY_PATH=/usr/local/compilers/Intel/parallel_studio_xe_2019.5/compiler/lib/mic:/usr/local/compilers/Intel/parallel_studio_xe_2019.5/mkl/lib/mic
24d24
< MV2_CPU_BINDING_POLICY=hybrid
26c26,27
< LD_LIBRARY_PATH=/usr/local/packages/mvapich2/2.3.3/axaxsfxv/lib:/usr/local/compilers/Intel/parallel_studio_xe_2019.5/compilers_and_libraries/linux/lib/intel64:/usr/local/compilers/Intel/parallel_studio_xe_2019.5/mkl/lib/intel64:/usr/local/compilers/Intel/parallel_studio_xe_2019.5/compilers_and_libraries/linux/lib/intel64:/home/jgflemin/.local/lib
---
> MV2_CPU_BINDING_POLICY=hybrid
> LS_COLORS=rs=0:di=01;34:ln=01;36:mh=00:pi=40;33:so=01;35:do=01;35:bd=40;33;01:cd=40;33;01:or=40;31;01:mi=01;05;37;41:su=37;41:sg=30;43:ca=30;41:tw=30;42:ow=34;42:st=37;44:ex=01;32:*.tar=01;31:*.tgz=01;31:*.arc=01;31:*.arj=01;31:*.taz=01;31:*.lha=01;31:*.lz4=01;31:*.lzh=01;31:*.lzma=01;31:*.tlz=01;31:*.txz=01;31:*.tzo=01;31:*.t7z=01;31:*.zip=01;31:*.z=01;31:*.Z=01;31:*.dz=01;31:*.gz=01;31:*.lrz=01;31:*.lz=01;31:*.lzo=01;31:*.xz=01;31:*.bz2=01;31:*.bz=01;31:*.tbz=01;31:*.tbz2=01;31:*.tz=01;31:*.deb=01;31:*.rpm=01;31:*.jar=01;31:*.war=01;31:*.ear=01;31:*.sar=01;31:*.rar=01;31:*.alz=01;31:*.ace=01;31:*.zoo=01;31:*.cpio=01;31:*.7z=01;31:*.rz=01;31:*.cab=01;31:*.jpg=01;35:*.jpeg=01;35:*.gif=01;35:*.bmp=01;35:*.pbm=01;35:*.pgm=01;35:*.ppm=01;35:*.tga=01;35:*.xbm=01;35:*.xpm=01;35:*.tif=01;35:*.tiff=01;35:*.png=01;35:*.svg=01;35:*.svgz=01;35:*.mng=01;35:*.pcx=01;35:*.mov=01;35:*.mpg=01;35:*.mpeg=01;35:*.m2v=01;35:*.mkv=01;35:*.webm=01;35:*.ogm=01;35:*.mp4=01;35:*.m4v=01;35:*.mp4v=01;35:*.vob=01;35:*.qt=01;35:*.nuv=01;35:*.wmv=01;35:*.asf=01;35:*.rm=01;35:*.rmvb=01;35:*.flc=01;35:*.avi=01;35:*.fli=01;35:*.flv=01;35:*.gl=01;35:*.dl=01;35:*.xcf=01;35:*.xwd=01;35:*.yuv=01;35:*.cgm=01;35:*.emf=01;35:*.axv=01;35:*.anx=01;35:*.ogv=01;35:*.ogx=01;35:*.aac=01;36:*.au=01;36:*.flac=01;36:*.mid=01;36:*.midi=01;36:*.mka=01;36:*.mp3=01;36:*.mpc=01;36:*.ogg=01;36:*.ra=01;36:*.wav=01;36:*.axa=01;36:*.oga=01;36:*.spx=01;36:*.xspf=01;36:
28d28
< LS_COLORS=rs=0:di=38;5;27:ln=38;5;51:mh=44;38;5;15:pi=40;38;5;11:so=38;5;13:do=38;5;5:bd=48;5;232;38;5;11:cd=48;5;232;38;5;3:or=48;5;232;38;5;9:mi=05;48;5;232;38;5;15:su=48;5;196;38;5;15:sg=48;5;11;38;5;16:ca=48;5;196;38;5;226:tw=48;5;10;38;5;16:ow=48;5;10;38;5;21:st=48;5;21;38;5;15:ex=38;5;34:*.tar=38;5;9:*.tgz=38;5;9:*.arc=38;5;9:*.arj=38;5;9:*.taz=38;5;9:*.lha=38;5;9:*.lz4=38;5;9:*.lzh=38;5;9:*.lzma=38;5;9:*.tlz=38;5;9:*.txz=38;5;9:*.tzo=38;5;9:*.t7z=38;5;9:*.zip=38;5;9:*.z=38;5;9:*.Z=38;5;9:*.dz=38;5;9:*.gz=38;5;9:*.lrz=38;5;9:*.lz=38;5;9:*.lzo=38;5;9:*.xz=38;5;9:*.bz2=38;5;9:*.bz=38;5;9:*.tbz=38;5;9:*.tbz2=38;5;9:*.tz=38;5;9:*.deb=38;5;9:*.rpm=38;5;9:*.jar=38;5;9:*.war=38;5;9:*.ear=38;5;9:*.sar=38;5;9:*.rar=38;5;9:*.alz=38;5;9:*.ace=38;5;9:*.zoo=38;5;9:*.cpio=38;5;9:*.7z=38;5;9:*.rz=38;5;9:*.cab=38;5;9:*.jpg=38;5;13:*.jpeg=38;5;13:*.gif=38;5;13:*.bmp=38;5;13:*.pbm=38;5;13:*.pgm=38;5;13:*.ppm=38;5;13:*.tga=38;5;13:*.xbm=38;5;13:*.xpm=38;5;13:*.tif=38;5;13:*.tiff=38;5;13:*.png=38;5;13:*.svg=38;5;13:*.svgz=38;5;13:*.mng=38;5;13:*.pcx=38;5;13:*.mov=38;5;13:*.mpg=38;5;13:*.mpeg=38;5;13:*.m2v=38;5;13:*.mkv=38;5;13:*.webm=38;5;13:*.ogm=38;5;13:*.mp4=38;5;13:*.m4v=38;5;13:*.mp4v=38;5;13:*.vob=38;5;13:*.qt=38;5;13:*.nuv=38;5;13:*.wmv=38;5;13:*.asf=38;5;13:*.rm=38;5;13:*.rmvb=38;5;13:*.flc=38;5;13:*.avi=38;5;13:*.fli=38;5;13:*.flv=38;5;13:*.gl=38;5;13:*.dl=38;5;13:*.xcf=38;5;13:*.xwd=38;5;13:*.yuv=38;5;13:*.cgm=38;5;13:*.emf=38;5;13:*.axv=38;5;13:*.anx=38;5;13:*.ogv=38;5;13:*.ogx=38;5;13:*.aac=38;5;45:*.au=38;5;45:*.flac=38;5;45:*.mid=38;5;45:*.midi=38;5;45:*.mka=38;5;45:*.mp3=38;5;45:*.mpc=38;5;45:*.ogg=38;5;45:*.ra=38;5;45:*.wav=38;5;45:*.axa=38;5;45:*.oga=38;5;45:*.spx=38;5;45:*.xspf=38;5;45:
31,33c31,55
< NLSPATH=/usr/local/compilers/Intel/parallel_studio_xe_2019.5/compiler/lib/intel64/locale/en_US:/usr/local/compilers/Intel/parallel_studio_xe_2019.5/mkl/lib/intel64/locale/en_US
< LANGUAGE_TERRITORY_modshare=en_US:1
< MODULES_LMCONFLICT=intel/19.0.5&intel:mvapich2/2.3.3/intel-19.0.5&mvapich2
---
> TERMCAP=SC|screen|VT 100/ANSI X3.64 virtual terminal:\
> 	:DO=\E[%dB:LE=\E[%dD:RI=\E[%dC:UP=\E[%dA:bs:bt=\E[Z:\
> 	:cd=\E[J:ce=\E[K:cl=\E[H\E[J:cm=\E[%i%d;%dH:ct=\E[3g:\
> 	:do=^J:nd=\E[C:pt:rc=\E8:rs=\Ec:sc=\E7:st=\EH:up=\EM:\
> 	:le=^H:bl=^G:cr=^M:it#8:ho=\E[H:nw=\EE:ta=^I:is=\E)0:\
> 	:li#109:co#235:am:xn:xv:LP:sr=\EM:al=\E[L:AL=\E[%dL:\
> 	:cs=\E[%i%d;%dr:dl=\E[M:DL=\E[%dM:dc=\E[P:DC=\E[%dP:\
> 	:im=\E[4h:ei=\E[4l:mi:IC=\E[%d@:ks=\E[?1h\E=:\
> 	:ke=\E[?1l\E>:vi=\E[?25l:ve=\E[34h\E[?25h:vs=\E[34l:\
> 	:ti=\E[?1049h:te=\E[?1049l:us=\E[4m:ue=\E[24m:so=\E[3m:\
> 	:se=\E[23m:mb=\E[5m:md=\E[1m:mr=\E[7m:me=\E[m:ms:\
> 	:Co#8:pa#64:AF=\E[3%dm:AB=\E[4%dm:op=\E[39;49m:AX:\
> 	:vb=\Eg:G0:as=\E(0:ae=\E(B:\
> 	:ac=\140\140aaffggjjkkllmmnnooppqqrrssttuuvvwwxxyyzz{{||}}~~..--++,,hhII00:\
> 	:po=\E[5i:pf=\E[4i:Km=\E[M:k0=\E[10~:k1=\EOP:k2=\EOQ:\
> 	:k3=\EOR:k4=\EOS:k5=\E[15~:k6=\E[17~:k7=\E[18~:\
> 	:k8=\E[19~:k9=\E[20~:k;=\E[21~:F1=\E[23~:F2=\E[24~:\
> 	:F3=\E[1;2P:F4=\E[1;2Q:F5=\E[1;2R:F6=\E[1;2S:\
> 	:F7=\E[15;2~:F8=\E[17;2~:F9=\E[18;2~:FA=\E[19;2~:kb=:\
> 	:K2=\EOE:kB=\E[Z:kF=\E[1;2B:kR=\E[1;2A:*4=\E[3;2~:\
> 	:*7=\E[1;2F:#2=\E[1;2H:#3=\E[2;2~:#4=\E[1;2D:%c=\E[6;2~:\
> 	:%e=\E[5;2~:%i=\E[1;2C:kh=\E[1~:@1=\E[1~:kH=\E[4~:\
> 	:@7=\E[4~:kN=\E[6~:kP=\E[5~:kI=\E[2~:kD=\E[3~:ku=\EOA:\
> 	:kd=\EOB:kr=\EOC:kl=\EOD:km:
> PATH=/home/jgflemin/bin:/home/jgflemin/bin:/usr/lib64/qt-3.3/bin:/usr/local/packages/mvapich2/2.3.3/axaxsfxv/bin:/usr/local/packages/Modules/4.2.5/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/local/bin:/usr/local/compilers/Intel/parallel_studio_xe_2019.5/compilers_and_libraries/linux/bin/intel64/:/opt/ibutils/bin:/opt/dell/srvadmin/bin:/home/jgflemin/.local/bin
35c57,58
< PATH=/home/jgflemin/bin:/usr/lib64/qt-3.3/bin:/usr/local/packages/mvapich2/2.3.3/axaxsfxv/bin:/usr/local/packages/Modules/4.2.5/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/local/bin:/usr/local/compilers/Intel/parallel_studio_xe_2019.5/compilers_and_libraries/linux/bin/intel64/:/opt/ibutils/bin:/opt/dell/srvadmin/bin:/home/jgflemin/.local/bin
---
> MODULES_LMCONFLICT=intel/19.0.5&intel:mvapich2/2.3.3/intel-19.0.5&mvapich2
> LANGUAGE_TERRITORY_modshare=en_US:1
36a60
> STY=11639.CPRA23v01c_nam_jgf
37a62
> PWD=/work/jgflemin/production/asgs
39d63
< PWD=/home/jgflemin
42d65
< MODULEPATH=/usr/local/packages/Modules/default/modulefiles/linux-rhel7-ivybridge
44c67
< KDEDIRS=/usr
---
> MODULEPATH=/usr/local/packages/Modules/default/modulefiles/linux-rhel7-ivybridge
45a69
> KDEDIRS=/usr
48d71
< LHPC_DEVELINTEL=/usr/local/compilers/Intel/parallel_studio_xe_2019.5/easybuild/intel-19.0.5-easybuild-devel
50,53c73
< LD_INCLUDE_PATH=/usr/local/compilers/Intel/parallel_studio_xe_2019.5/mkl/include
< PATH_modshare=/usr/sbin:1:/usr/local/packages/mvapich2/2.3.3/axaxsfxv/bin:1:/usr/bin:1:/usr/local/sbin:1:/usr/local/compilers/Intel/parallel_studio_xe_2019.5/compilers_and_libraries/linux/bin/intel64/:1:/usr/local/packages/Modules/4.2.5/bin:1:/usr/local/bin:1
< MODULES_LMCONFLICT_modshare=mvapich2/2.3.3/intel-19.0.5&mvapich2:1:intel/19.0.5&intel:1
< SHLVL=1
---
> LHPC_DEVELINTEL=/usr/local/compilers/Intel/parallel_studio_xe_2019.5/easybuild/intel-19.0.5-easybuild-devel
55c75,78
< MODULES_LMNOTUASKED=intel/19.0.5
---
> SHLVL=2
> MODULES_LMCONFLICT_modshare=mvapich2/2.3.3/intel-19.0.5&mvapich2:1:intel/19.0.5&intel:1
> PATH_modshare=/usr/sbin:1:/usr/local/packages/mvapich2/2.3.3/axaxsfxv/bin:1:/usr/bin:1:/usr/local/sbin:1:/usr/local/compilers/Intel/parallel_studio_xe_2019.5/compilers_and_libraries/linux/bin/intel64/:1:/usr/local/packages/Modules/4.2.5/bin:1:/usr/local/bin:1
> LD_INCLUDE_PATH=/usr/local/compilers/Intel/parallel_studio_xe_2019.5/mkl/include
57c80
< NLSPATH_modshare=/usr/local/compilers/Intel/parallel_studio_xe_2019.5/compiler/lib/intel64/locale/en_US:1:/usr/local/compilers/Intel/parallel_studio_xe_2019.5/mkl/lib/intel64/locale/en_US:1
---
> MODULES_LMNOTUASKED=intel/19.0.5
58a82
> NLSPATH_modshare=/usr/local/compilers/Intel/parallel_studio_xe_2019.5/compiler/lib/intel64/locale/en_US:1:/usr/local/compilers/Intel/parallel_studio_xe_2019.5/mkl/lib/intel64/locale/en_US:1
60,61d83
< QTLIB=/usr/lib64/qt-3.3/lib
< LD_LIBRARY_PATH_modshare=/usr/local/compilers/Intel/parallel_studio_xe_2019.5/compilers_and_libraries/linux/lib/intel64:1:/usr/local/compilers/Intel/parallel_studio_xe_2019.5/mkl/lib/intel64:1:/usr/local/packages/mvapich2/2.3.3/axaxsfxv/lib:1
63c85,87
< XDG_DATA_DIRS=/home/jgflemin/.local/share/flatpak/exports/share:/var/lib/flatpak/exports/share:/usr/local/share:/usr/share
---
> LD_LIBRARY_PATH_modshare=/usr/local/compilers/Intel/parallel_studio_xe_2019.5/compilers_and_libraries/linux/lib/intel64:1:/usr/local/compilers/Intel/parallel_studio_xe_2019.5/mkl/lib/intel64:1:/usr/local/packages/mvapich2/2.3.3/axaxsfxv/lib:1
> QTLIB=/usr/lib64/qt-3.3/lib
> WINDOW=0
65c89
< LHPC_ROOTINTEL=/usr/local/compilers/Intel/parallel_studio_xe_2019.5
---
> XDG_DATA_DIRS=/home/jgflemin/.local/share/flatpak/exports/share:/var/lib/flatpak/exports/share:/usr/local/share:/usr/share
67,68c91
< LESSOPEN=||/usr/bin/lesspipe.sh %s
< MV2_USE_RDMA_CM=0
---
> LHPC_ROOTINTEL=/usr/local/compilers/Intel/parallel_studio_xe_2019.5
69a93,94
> MV2_USE_RDMA_CM=0
> LESSOPEN=||/usr/bin/lesspipe.sh %s
71d95
< CMAKE_PREFIX_PATH=/usr/local/packages/mvapich2/2.3.3/axaxsfxv/
72a97
> CMAKE_PREFIX_PATH=/usr/local/packages/mvapich2/2.3.3/axaxsfxv/