[Nek5000-users] maketools all fails at postnek on RHEL6.4
nek5000-users at lists.mcs.anl.gov
nek5000-users at lists.mcs.anl.gov
Wed Dec 14 09:57:03 CST 2016
Stefan, this zip provides the following and appears to generate more tools before one error shown below at the prenek stage. This may be a lead on this new error ... https://www.technovelty.org/c/relocation-truncated-to-fit-wtf.html
[user at rhel64 tools]$ ./maketools all /nfs/home/user/Nek5000
----------------------
Make genbox...
----------------------
make[1]: Entering directory `/home/user/Nek5000-release-v16.0.0/tools/genbox'
gfortran -c -fdefault-real-8 genbox.f
gcc -c -DUNDERSCORE byte.c
gfortran -fdefault-real-8 -o /nfs/home/user/Nek5000/genbox genbox.o byte.o
make[1]: Leaving directory `/home/user/Nek5000-release-v16.0.0/tools/genbox'
----------------------
Make int_tp...
----------------------
make[1]: Entering directory `/home/user/Nek5000-release-v16.0.0/tools/int_tp'
gfortran -c int_tp.f
gfortran -c ../../core/speclib.f
gfortran -c mxm44f2.f
gcc -c -DUNDERSCORE byte.c
gfortran -c int_tp_gbox.f
gfortran -o /nfs/home/user/Nek5000/int_tp int_tp.o speclib.o mxm44f2.o byte.o int_tp_gbox.o
make[1]: Leaving directory `/home/user/Nek5000-release-v16.0.0/tools/int_tp'
----------------------
Make n2to3...
----------------------
make[1]: Entering directory `/home/user/Nek5000-release-v16.0.0/tools/n2to3'
gfortran -c n2to3.f
gcc -c -DUNDERSCORE byte.c
gfortran -o /nfs/home/user/Nek5000/n2to3 n2to3.o byte.o
make[1]: Leaving directory `/home/user/Nek5000-release-v16.0.0/tools/n2to3'
----------------------
Make postnek...
----------------------
make[1]: Entering directory `/home/user/Nek5000-release-v16.0.0/tools/postnek'
gfortran -c postnek.f
gfortran -c postnek2.f
gfortran -c postnek3.f
postnek3.f:1552.20:
COMMON /CTMP4/ wk(LXYZ,3,3)
1
Warning: Named COMMON block 'ctmp4' at (1) shall be of the same size
gfortran -c postnek5.f
postnek5.f:711.21:
COMMON /ccdiag/ iee,iii
1
Warning: Named COMMON block 'ccdiag' at (1) shall be of the same size
gfortran -c postnek6.f
gfortran -c tsort.f
gfortran -c postnek8.f
devices.inc:22.19:
Included at basics.inc:168:
Included at postnek8.f:96:
COMMON/SCALE/XFAC ,YFAC ,XZERO ,YZERO
1
Warning: Named COMMON block 'scale' at (1) shall be of the same size
gfortran -c postnek9.f
gfortran -c plot.f
gfortran -c getfld.f
gfortran -c legend.f
gfortran -c userf.f
userf.f:1282.21:
common /rlobjs/ x_l_objs(mopts),y_l_objs(mopts),z_l_objs(mopts)
1
Warning: Named COMMON block 'rlobjs' at (1) shall be of the same size
userf.f:1816.21:
common /rlobjs/ avg(6,0:mopts-1,3)
1
Warning: Named COMMON block 'rlobjs' at (1) shall be of the same size
userf.f:5261.20:
common /ctmp1/ uavg(nxm*nelm),vavg(nxm*nelm),wavg(nxm*nelm)
1
Warning: Named COMMON block 'ctmp1' at (1) shall be of the same size
gcc -c -DUNDERSCORE revert.c
gfortran -c trap.f
gfortran -c animate.f
gfortran -c genxyz.f
gfortran -c screen.f
gfortran -c g3d.f
gfortran -c subs.f
gfortran -c xinterface.f
gfortran -c locglob.f
gfortran -c postnek5a.f
gfortran -c ../../core/3rd_party/blas.f
../../core/3rd_party/blas.f:9764.15:
GO TO IGO,(120,150,180,210)
1
Warning: Deleted feature: Assigned GOTO statement at (1)
../../core/3rd_party/blas.f:9770.72:
ASSIGN 120 TO IGO
1
Warning: Deleted feature: ASSIGN statement at (1)
../../core/3rd_party/blas.f:9782.72:
ASSIGN 150 TO IGO
1
Warning: Deleted feature: ASSIGN statement at (1)
../../core/3rd_party/blas.f:9795.72:
ASSIGN 180 TO IGO
1
Warning: Deleted feature: ASSIGN statement at (1)
../../core/3rd_party/blas.f:9806.72:
ASSIGN 210 TO IGO
1
Warning: Deleted feature: ASSIGN statement at (1)
../../core/3rd_party/blas.f:17277.15:
GO TO IGO,(120,150,180,210)
1
Warning: Deleted feature: Assigned GOTO statement at (1)
../../core/3rd_party/blas.f:17283.72:
ASSIGN 120 TO IGO
1
Warning: Deleted feature: ASSIGN statement at (1)
../../core/3rd_party/blas.f:17295.72:
ASSIGN 150 TO IGO
1
Warning: Deleted feature: ASSIGN statement at (1)
../../core/3rd_party/blas.f:17308.72:
ASSIGN 180 TO IGO
1
Warning: Deleted feature: ASSIGN statement at (1)
../../core/3rd_party/blas.f:17319.72:
ASSIGN 210 TO IGO
1
Warning: Deleted feature: ASSIGN statement at (1)
gcc -c -O2 -DUNDERSCORE xdriver.c
gfortran -c scrdmp.f
gfortran -c coef.f
gfortran -c postnek7.f
gfortran -c speclib.f
gfortran -c mxm.f
gcc -c -DUNDERSCORE byte.c
gfortran -c ssyev.f
gfortran -c iolib.f
gfortran -o /nfs/home/user/Nek5000/postx postnek.o postnek2.o postnek3.o postnek5.o postnek6.o tsort.o postnek8.o postnek9.o plot.o getfld.o legend.o userf.o revert.o trap.o animate.o genxyz.o screen.o g3d.o subs.o xinterface.o locglob.o postnek5a.o blas.o xdriver.o scrdmp.o coef.o postnek7.o speclib.o mxm.o byte.o ssyev.o iolib.o -L/usr/lib/X11 -lX11 -lm
Linux
2.6.32-358.el6.x86_64
gfortran -c iolib_no_graph.f
gfortran -o /nfs/home/user/Nek5000/postex postnek.o postnek2.o postnek3.o postnek5.o postnek6.o tsort.o postnek8.o postnek9.o plot.o getfld.o legend.o userf.o revert.o trap.o animate.o genxyz.o screen.o g3d.o subs.o xinterface.o locglob.o postnek5a.o blas.o xdriver.o scrdmp.o coef.o postnek7.o speclib.o mxm.o byte.o ssyev.o iolib_no_graph.o -L/usr/lib/X11 -lX11 -lm
make[1]: Leaving directory `/home/user/Nek5000-release-v16.0.0/tools/postnek'
----------------------
Make reatore2...
----------------------
make[1]: Entering directory `/home/user/Nek5000-release-v16.0.0/tools/reatore2'
gfortran -c reatore2.f
gcc -c -DUNDERSCORE byte.c
gfortran -c strings.f
gfortran -o /nfs/home/user/Nek5000/reatore2 reatore2.o byte.o strings.o
gfortran -c re2torea.f
gfortran -o /nfs/home/user/Nek5000/re2torea re2torea.o byte.o strings.o
make[1]: Leaving directory `/home/user/Nek5000-release-v16.0.0/tools/reatore2'
----------------------
Make genmap...
----------------------
make[1]: Entering directory `/home/user/Nek5000-release-v16.0.0/tools/genmap'
gfortran -c -fdefault-real-8 genmap.f
genmap.f:3054.22:
common /carrayw/ w1 (lpts) , w2 (lpts)
1
Warning: Named COMMON block 'carrayw' at (1) shall be of the same size
genmap.f:4017.22:
common /arrayi2/ jdual(32*lelm) , vdual(32*lelm)
1
Warning: Named COMMON block 'arrayi2' at (1) shall be of the same size
gcc -c -DUNDERSCORE ../../core/byte.c
gfortran -fdefault-real-8 -o /nfs/home/user/Nek5000/genmap genmap.o byte.o
make[1]: Leaving directory `/home/user/Nek5000-release-v16.0.0/tools/genmap'
----------------------
Make nekmerge...
----------------------
make[1]: Entering directory `/home/user/Nek5000-release-v16.0.0/tools/nekmerge'
gfortran -c nekmerge.f
gfortran -c reader.f
gcc -c -DUNDERSCORE byte.c
gfortran -c strings.f
gfortran -c tsort.f
gfortran -o /nfs/home/user/Nek5000/nekmerge nekmerge.o reader.o byte.o strings.o tsort.o
make[1]: Leaving directory `/home/user/Nek5000-release-v16.0.0/tools/nekmerge'
----------------------
Make prenek...
----------------------
make[1]: Entering directory `/home/user/Nek5000-release-v16.0.0/tools/prenek'
gfortran -c prenek.f
gfortran -c curve.f
gfortran -c edit.f
gfortran -c build.f
gfortran -c build1.f
gfortran -c build2.f
build2.f:323.10:
xcs(3,1) = 0.
1
Warning: Array reference at (1) is out of bounds (3 > 2) in dimension 1
build2.f:324.10:
ycs(3,1) = radius
1
Warning: Array reference at (1) is out of bounds (3 > 2) in dimension 1
build2.f:325.10:
zcs(3,1) = 0.
1
Warning: Array reference at (1) is out of bounds (3 > 2) in dimension 1
build2.f:332.20:
common /ctmp0/ sphctr(3),xcs(4,24),ycs(4,24),zcs(4,24)
1
Warning: Named COMMON block 'ctmp0' at (1) shall be of the same size
gfortran -c bound.f
gfortran -c plot.f
gfortran -c xinterface.f
gfortran -c glomod.f
glomod.f:2120.9:
ja(2) = w(2,1)
1
Warning: Array reference at (1) is out of bounds (2 > 1) in dimension 1
gfortran -c legend.f
gfortran -c vprops.f
gfortran -c iolib.f
gfortran -c subs.f
gfortran -c zipper2.f
zipper2.f:1580.20:
COMMON /CTMP2/ XP(NXM3),YP(NXM3),ZP(NXM3),RRL(3)
1
Warning: Named COMMON block 'ctmp2' at (1) shall be of the same size
zipper2.f:2849.20:
COMMON /CTMP2/ XP(NXM3),YP(NXM3),ZP(NXM3),RRL(3)
1
Warning: Named COMMON block 'ctmp2' at (1) shall be of the same size
zipper2.f:4465.20:
common /ctmp0/ jx(nxm*3),jyt(nym*3),jzt(nzm*3)
1
Warning: Named COMMON block 'ctmp0' at (1) shall be of the same size
zipper2.f:4464.20:
common /ctmp2/ xp(nxm3),yp(nxm3),zp(nxm3),wk(ldw)
1
Warning: Named COMMON block 'ctmp2' at (1) shall be of the same size
zipper2.f:4612.20:
common /ctmp0/ xcb(2,2,2),ycb(2,2,2),zcb(2,2,2),w(ldw)
1
Warning: Named COMMON block 'ctmp0' at (1) shall be of the same size
gfortran -c postnek6.f
gfortran -c screen.f
gcc -c -DUNDERSCORE -Dr8 revert.c
gfortran -c crs.f
gfortran -c mxm.f
gcc -c -DUNDERSCORE -Dr8 xdriver.c
gfortran -o /nfs/home/user/Nek5000/prex prenek.o curve.o edit.o build.o build1.o build2.o bound.o plot.o xinterface.o glomod.o legend.o vprops.o iolib.o subs.o zipper2.o postnek6.o screen.o revert.o crs.o mxm.o xdriver.o -L/usr/lib/X11 -lX11 -lm
curve.o: In function `hex_transition_3d_e_':
curve.f:(.text+0x560a): relocation truncated to fit: R_X86_64_PC32 against symbol `ctmp2_' defined in COMMON section in zipper2.o
curve.f:(.text+0x567f): relocation truncated to fit: R_X86_64_PC32 against symbol `ctmp2_' defined in COMMON section in zipper2.o
curve.f:(.text+0x56ac): relocation truncated to fit: R_X86_64_PC32 against symbol `ctmp2_' defined in COMMON section in zipper2.o
curve.f:(.text+0x56d9): relocation truncated to fit: R_X86_64_PC32 against symbol `ctmp2_' defined in COMMON section in zipper2.o
curve.o: In function `hexagon_refine_e_':
curve.f:(.text+0x5ca0): relocation truncated to fit: R_X86_64_PC32 against symbol `ctmp2_' defined in COMMON section in zipper2.o
curve.f:(.text+0x5d3a): relocation truncated to fit: R_X86_64_PC32 against symbol `ctmp2_' defined in COMMON section in zipper2.o
curve.f:(.text+0x5d8c): relocation truncated to fit: R_X86_64_PC32 against symbol `ctmp2_' defined in COMMON section in zipper2.o
build.o: In function `new_out_':
build.f:(.text+0xba7f): relocation truncated to fit: R_X86_64_32S against symbol `c_xyz_' defined in COMMON section in build.o
build.f:(.text+0xbabc): relocation truncated to fit: R_X86_64_32S against symbol `c_xyz_' defined in COMMON section in build.o
build.f:(.text+0xbaf9): relocation truncated to fit: R_X86_64_32S against symbol `c_xyz_' defined in COMMON section in build.o
build.f:(.text+0xbc7c): additional relocation overflows omitted from the output
glomod.o: In function `runlapsm2d_':
glomod.f:(.text+0xbc53): undefined reference to `col2_'
glomod.f:(.text+0xbc75): undefined reference to `col2_'
glomod.f:(.text+0xbcf0): undefined reference to `col2_'
glomod.f:(.text+0xbd0f): undefined reference to `col2_'
glomod.o: In function `runoptsm2d_':
glomod.f:(.text+0xc25e): undefined reference to `col2_'
glomod.o:glomod.f:(.text+0xc28f): more undefined references to `col2_' follow
collect2: ld returned 1 exit status
make[1]: *** [prex] Error 1
make[1]: Leaving directory `/home/user/Nek5000-release-v16.0.0/tools/prenek'
make: *** [all] Error 1
[user at rhel64 tools]$ ls -la /nfs/home/user/Nek5000
total 4312
drwxr-xr-x 2 user users 4096 Dec 14 10:37 .
drwx------. 39 user ansys 4096 Dec 14 10:36 ..
-rwxr-xr-x 1 user users 122691 Dec 14 10:37 genbox
-rwxr-xr-x 1 user users 119786 Dec 14 10:37 genmap
-rwxr-xr-x 1 user users 168611 Dec 14 10:37 int_tp
-rwxr-xr-x 1 user users 74445 Dec 14 10:37 n2to3
-rwxr-xr-x 1 user users 54406 Dec 14 10:37 nekmerge
-rwxr-xr-x 1 user users 1896156 Dec 14 10:37 postex
-rwxr-xr-x 1 user users 1897203 Dec 14 10:37 postx
-rwxr-xr-x 1 user users 28257 Dec 14 10:37 re2torea
-rwxr-xr-x 1 user users 26682 Dec 14 10:37 reatore2
[user at rhel64 tools]$
-----Original Message-----
From: nek5000-users-bounces at lists.mcs.anl.gov [mailto:nek5000-users-bounces at lists.mcs.anl.gov] On Behalf Of nek5000-users at lists.mcs.anl.gov
Sent: Wednesday, December 14, 2016 12:10 PM
To: nek5000-users at lists.mcs.anl.gov
Subject: Re: [Nek5000-users] maketools all fails at postnek on RHEL6.4
Can you try again with release/v16.0.0 (https://github.com/Nek5000/Nek5000/archive/release/v16.0.0.zip)
Cheers,
Stefan
-----Original message-----
> From:nek5000-users at lists.mcs.anl.gov <nek5000-users at lists.mcs.anl.gov>
> Sent: Wednesday 14th December 2016 18:06
> To: nek5000-users at lists.mcs.anl.gov
> Subject: Re: [Nek5000-users] maketools all fails at postnek on RHEL6.4
>
> Using the tarball at
> https://github.com/Nek5000/nek5000/archive/master.tar.gz to compile
> locally on my RHEL6.4 server. During maketools event, only the genmap
> and n2to3 tools are compiled and the make event fails out as shown
> below. Is this attributed to BIGMEM=true in maketools, or something
> else? Can anyone help? Error and gcc/gfortran information below
> Thanks Richard P
> [user at rhel64 tools]$ gedit maketools
> [user at rhel64 tools]$ ./maketools all /nfs/home/user/Nek5000
> ----------------------
> Make genmap...
> ----------------------
> make[1]: Entering directory `/home/user/Nek5000-master/tools/genmap'
> gfortran -mcmodel=medium -fdefault-real-8 -o
> /nfs/home/user/Nek5000/genmap genmap.o byte.o
> make[1]: Leaving directory `/home/user/Nek5000-master/tools/genmap'
> ----------------------
> Make n2to3...
> ----------------------
> make[1]: Entering directory `/home/user/Nek5000-master/tools/n2to3'
> gfortran -mcmodel=medium -o /nfs/home/user/Nek5000/n2to3 n2to3.o
> byte.o
> make[1]: Leaving directory `/home/user/Nek5000-master/tools/n2to3'
> ----------------------
> Make postnek...
> ----------------------
> make[1]: Entering directory `/home/user/Nek5000-master/tools/postnek'
> gfortran -mcmodel=medium -c postnek.f
> postnek.f:1977.19:
> ifbswap = if_byte_swap_test(test)
> 1
> Warning: Extension: Conversion from INTEGER(4) to LOGICAL(4) at (1)
> gfortran -mcmodel=medium -c postnek2.f gfortran -mcmodel=medium -c
> postnek3.f
> postnek3.f:1552.20:
> COMMON /CTMP4/ wk(LXYZ,3,3)
> 1
> Warning: Named COMMON block 'ctmp4' at (1) shall be of the same size
> gfortran -mcmodel=medium -c postnek5.f
> postnek5.f:711.21:
> COMMON /ccdiag/ iee,iii
> 1
> Warning: Named COMMON block 'ccdiag' at (1) shall be of the same size
> gfortran -mcmodel=medium -c postnek6.f gfortran -mcmodel=medium -c
> tsort.f gfortran -mcmodel=medium -c postnek8.f
> devices.inc:22.19:
> Included at basics.inc:168:
> Included at postnek8.f:96:
> COMMON/SCALE/XFAC ,YFAC ,XZERO ,YZERO
> 1
> Warning: Named COMMON block 'scale' at (1) shall be of the same size
> gfortran -mcmodel=medium -c postnek9.f gfortran -mcmodel=medium -c
> plot.f gfortran -mcmodel=medium -c getfld.f gfortran
> -mcmodel=medium -c legend.f gfortran -mcmodel=medium -c userf.f
> userf.f:1282.21:
> common /rlobjs/
> x_l_objs(mopts),y_l_objs(mopts),z_l_objs(mopts)
> 1
> Warning: Named COMMON block 'rlobjs' at (1) shall be of the same size
> userf.f:1816.21:
> common /rlobjs/ avg(6,0:mopts-1,3)
> 1
> Warning: Named COMMON block 'rlobjs' at (1) shall be of the same size
> userf.f:5261.20:
> common /ctmp1/ uavg(nxm*nelm),vavg(nxm*nelm),wavg(nxm*nelm)
> 1
> Warning: Named COMMON block 'ctmp1' at (1) shall be of the same size
> gfortran -mcmodel=medium -c trap.f gfortran -mcmodel=medium -c
> animate.f gfortran -mcmodel=medium -c genxyz.f gfortran
> -mcmodel=medium -c screen.f gfortran -mcmodel=medium -c g3d.f
> gfortran -mcmodel=medium -c subs.f gfortran -mcmodel=medium -c
> xinterface.f gfortran -mcmodel=medium -c locglob.f gfortran
> -mcmodel=medium -c postnek5a.f gfortran -mcmodel=medium -c
> ../../nek/3rd_party/blas.f
> gfortran: ../../nek/3rd_party/blas.f: No such file or directory
> gfortran: no input files
> make[1]: *** [blas.o] Error 1
> make[1]: Leaving directory `/home/user/Nek5000-master/tools/postnek'
> make: *** [all] Error 1
> ###########gcc and gfortran details for server##########
> [user at rhel64 tools]$ rpm -qa | grep gcc
> gcc-4.4.7-3.el6.x86_64
> compat-gcc-34-3.4.6-19.el6.x86_64
> gcc-gfortran-4.4.7-3.el6.x86_64
> libgcc-4.4.7-3.el6.i686
> gcc-c-4.4.7-3.el6.x86_64
> libgcc-4.4.7-3.el6.x86_64
> [user at rhel64 tools]$ rpm -qa | grep gfortran
> gcc-gfortran-4.4.7-3.el6.x86_64
> libgfortran-4.4.7-3.el6.x86_64
> compat-libgfortran-41-4.1.2-39.el6.x86_64
> Richard B Powell
> Technical Architect II
> Operations/Server Engineering
> AREVA, Inc.
> 3315 Old Forest Road OF-60
> Lynchburg, VA 24501
> Phone: 1 434-832-3894
> Fax: 1 434-382-3894
> _______________________________________________
> Nek5000-users mailing list
> Nek5000-users at lists.mcs.anl.gov
> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users
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