On Fri, 5 Sep 2014, Francois Bissey wrote:
In
"/home/jm58660/r-compile-test/sage-6.3/local/var/tmp/sage/build/r-3.1.1.p0/src/src/main"
What does
gcc -std=gnu99 -Wl,--export-dynamic -fopenmp
-L/home/jm58660/r-compile-test/sage-6.3/local/lib/ -o R.bin Rmain.o
-L../../lib -lR -Wl,--verbose
says.
It says quite much:
GNU ld version 2.23.2
Supported emulations:
elf_x86_64
elf32_x86_64
elf_i386
i386linux
elf_l1om
elf_k1om
using internal linker script:
==================================================
/* Script for -z combreloc: combine and sort reloc sections */
OUTPUT_FORMAT("elf64-x86-64", "elf64-x86-64",
"elf64-x86-64")
OUTPUT_ARCH(i386:x86-64)
ENTRY(_start)
SEARCH_DIR("/usr/x86_64-redhat-linux/lib64");
SEARCH_DIR("/usr/local/lib64"); SEARCH_DIR("/lib64");
SEARCH_DIR("/usr/lib64"); SEARCH_DIR("/usr/x86_64-redhat-linux/lib");
SEARCH_DIR("/usr/lib64"); SEARCH_DIR("/usr/local/lib");
SEARCH_DIR("/lib"); SEARCH_DIR("/usr/lib");
SECTIONS
{
/* Read-only sections, merged into text segment: */
PROVIDE (__executable_start = SEGMENT_START("text-segment", 0x400000));
. = SEGMENT_START("text-segment", 0x400000) + SIZEOF_HEADERS;
.interp : { *(.interp) }
.note.gnu.build-id : { *(.note.gnu.build-id) }
.hash : { *(.hash) }
.gnu.hash : { *(.gnu.hash) }
.dynsym : { *(.dynsym) }
.dynstr : { *(.dynstr) }
.gnu.version : { *(.gnu.version) }
.gnu.version_d : { *(.gnu.version_d) }
.gnu.version_r : { *(.gnu.version_r) }
.rela.dyn :
{
*(.rela.init)
*(.rela.text .rela.text.* .rela.gnu.linkonce.t.*)
*(.rela.fini)
*(.rela.rodata .rela.rodata.* .rela.gnu.linkonce.r.*)
*(.rela.data .rela.data.* .rela.gnu.linkonce.d.*)
*(.rela.tdata .rela.tdata.* .rela.gnu.linkonce.td.*)
*(.rela.tbss .rela.tbss.* .rela.gnu.linkonce.tb.*)
*(.rela.ctors)
*(.rela.dtors)
*(.rela.got)
*(.rela.bss .rela.bss.* .rela.gnu.linkonce.b.*)
*(.rela.ldata .rela.ldata.* .rela.gnu.linkonce.l.*)
*(.rela.lbss .rela.lbss.* .rela.gnu.linkonce.lb.*)
*(.rela.lrodata .rela.lrodata.* .rela.gnu.linkonce.lr.*)
*(.rela.ifunc)
}
.rela.plt :
{
*(.rela.plt)
PROVIDE_HIDDEN (__rela_iplt_start = .);
*(.rela.iplt)
PROVIDE_HIDDEN (__rela_iplt_end = .);
}
.init :
{
KEEP (*(SORT_NONE(.init)))
}
.plt : { *(.plt) *(.iplt) }
.text :
{
*(.text.unlikely .text.*_unlikely)
*(.text.exit .text.exit.*)
*(.text.startup .text.startup.*)
*(.text.hot .text.hot.*)
*(.text .stub .text.* .gnu.linkonce.t.*)
/* .gnu.warning sections are handled specially by elf32.em. */
*(.gnu.warning)
}
.fini :
{
KEEP (*(SORT_NONE(.fini)))
}
PROVIDE (__etext = .);
PROVIDE (_etext = .);
PROVIDE (etext = .);
.rodata : { *(.rodata .rodata.* .gnu.linkonce.r.*) }
.rodata1 : { *(.rodata1) }
.eh_frame_hdr : { *(.eh_frame_hdr) }
.eh_frame : ONLY_IF_RO { KEEP (*(.eh_frame)) }
.gcc_except_table : ONLY_IF_RO { *(.gcc_except_table
.gcc_except_table.*) }
/* These sections are generated by the Sun/Oracle C++ compiler. */
.exception_ranges : ONLY_IF_RO { *(.exception_ranges
.exception_ranges*) }
/* Adjust the address for the data segment. We want to adjust up to
the same address within the page on the next page up. */
. = ALIGN (CONSTANT (MAXPAGESIZE)) - ((CONSTANT (MAXPAGESIZE) - .) &
(CONSTANT (MAXPAGESIZE) - 1)); . = DATA_SEGMENT_ALIGN (CONSTANT
(MAXPAGESIZE), CONSTANT (COMMONPAGESIZE));
/* Exception handling */
.eh_frame : ONLY_IF_RW { KEEP (*(.eh_frame)) }
.gcc_except_table : ONLY_IF_RW { *(.gcc_except_table
.gcc_except_table.*) }
.exception_ranges : ONLY_IF_RW { *(.exception_ranges
.exception_ranges*) }
/* Thread Local Storage sections */
.tdata : { *(.tdata .tdata.* .gnu.linkonce.td.*) }
.tbss : { *(.tbss .tbss.* .gnu.linkonce.tb.*) *(.tcommon) }
.preinit_array :
{
PROVIDE_HIDDEN (__preinit_array_start = .);
KEEP (*(.preinit_array))
PROVIDE_HIDDEN (__preinit_array_end = .);
}
.init_array :
{
PROVIDE_HIDDEN (__init_array_start = .);
KEEP (*(SORT_BY_INIT_PRIORITY(.init_array.*)
SORT_BY_INIT_PRIORITY(.ctors.*)))
KEEP (*(.init_array))
KEEP (*(EXCLUDE_FILE (*crtbegin.o *crtbegin?.o *crtend.o *crtend?.o )
.ctors))
PROVIDE_HIDDEN (__init_array_end = .);
}
.fini_array :
{
PROVIDE_HIDDEN (__fini_array_start = .);
KEEP (*(SORT_BY_INIT_PRIORITY(.fini_array.*)
SORT_BY_INIT_PRIORITY(.dtors.*)))
KEEP (*(.fini_array))
KEEP (*(EXCLUDE_FILE (*crtbegin.o *crtbegin?.o *crtend.o *crtend?.o )
.dtors))
PROVIDE_HIDDEN (__fini_array_end = .);
}
.ctors :
{
/* gcc uses crtbegin.o to find the start of
the constructors, so we make sure it is
first. Because this is a wildcard, it
doesn't matter if the user does not
actually link against crtbegin.o; the
linker won't look for a file to match a
wildcard. The wildcard also means that it
doesn't matter which directory crtbegin.o
is in. */
KEEP (*crtbegin.o(.ctors))
KEEP (*crtbegin?.o(.ctors))
/* We don't want to include the .ctor section from
the crtend.o file until after the sorted ctors.
The .ctor section from the crtend file contains the
end of ctors marker and it must be last */
KEEP (*(EXCLUDE_FILE (*crtend.o *crtend?.o ) .ctors))
KEEP (*(SORT(.ctors.*)))
KEEP (*(.ctors))
}
.dtors :
{
KEEP (*crtbegin.o(.dtors))
KEEP (*crtbegin?.o(.dtors))
KEEP (*(EXCLUDE_FILE (*crtend.o *crtend?.o ) .dtors))
KEEP (*(SORT(.dtors.*)))
KEEP (*(.dtors))
}
.jcr : { KEEP (*(.jcr)) }
.data.rel.ro : { *(.data.rel.ro.local* .gnu.linkonce.d.rel.ro.local.*)
*(.data.rel.ro .data.rel.ro.* .gnu.linkonce.d.rel.ro.*) }
.dynamic : { *(.dynamic) }
.got : { *(.got) *(.igot) }
. = DATA_SEGMENT_RELRO_END (SIZEOF (.got.plt) >= 24 ? 24 : 0, .);
.got.plt : { *(.got.plt) *(.igot.plt) }
.data :
{
*(.data .data.* .gnu.linkonce.d.*)
SORT(CONSTRUCTORS)
}
.data1 : { *(.data1) }
_edata = .; PROVIDE (edata = .);
. = .;
__bss_start = .;
.bss :
{
*(.dynbss)
*(.bss .bss.* .gnu.linkonce.b.*)
*(COMMON)
/* Align here to ensure that the .bss section occupies space up to
_end. Align after .bss to ensure correct alignment even if the
.bss section disappears because there are no input sections.
FIXME: Why do we need it? When there is no .bss section, we don't
pad the .data section. */
. = ALIGN(. != 0 ? 64 / 8 : 1);
}
.lbss :
{
*(.dynlbss)
*(.lbss .lbss.* .gnu.linkonce.lb.*)
*(LARGE_COMMON)
}
. = ALIGN(64 / 8);
.lrodata ALIGN(CONSTANT (MAXPAGESIZE)) + (. & (CONSTANT (MAXPAGESIZE)
- 1)) :
{
*(.lrodata .lrodata.* .gnu.linkonce.lr.*)
}
.ldata ALIGN(CONSTANT (MAXPAGESIZE)) + (. & (CONSTANT (MAXPAGESIZE) -
1)) :
{
*(.ldata .ldata.* .gnu.linkonce.l.*)
. = ALIGN(. != 0 ? 64 / 8 : 1);
}
. = ALIGN(64 / 8);
_end = .; PROVIDE (end = .);
. = DATA_SEGMENT_END (.);
/* Stabs debugging sections. */
.stab 0 : { *(.stab) }
.stabstr 0 : { *(.stabstr) }
.stab.excl 0 : { *(.stab.excl) }
.stab.exclstr 0 : { *(.stab.exclstr) }
.stab.index 0 : { *(.stab.index) }
.stab.indexstr 0 : { *(.stab.indexstr) }
.comment 0 : { *(.comment) }
/* DWARF debug sections.
Symbols in the DWARF debugging sections are relative to the beginning
of the section so we begin them at 0. */
/* DWARF 1 */
.debug 0 : { *(.debug) }
.line 0 : { *(.line) }
/* GNU DWARF 1 extensions */
.debug_srcinfo 0 : { *(.debug_srcinfo) }
.debug_sfnames 0 : { *(.debug_sfnames) }
/* DWARF 1.1 and DWARF 2 */
.debug_aranges 0 : { *(.debug_aranges) }
.debug_pubnames 0 : { *(.debug_pubnames) }
/* DWARF 2 */
.debug_info 0 : { *(.debug_info .gnu.linkonce.wi.*) }
.debug_abbrev 0 : { *(.debug_abbrev) }
.debug_line 0 : { *(.debug_line) }
.debug_frame 0 : { *(.debug_frame) }
.debug_str 0 : { *(.debug_str) }
.debug_loc 0 : { *(.debug_loc) }
.debug_macinfo 0 : { *(.debug_macinfo) }
/* SGI/MIPS DWARF 2 extensions */
.debug_weaknames 0 : { *(.debug_weaknames) }
.debug_funcnames 0 : { *(.debug_funcnames) }
.debug_typenames 0 : { *(.debug_typenames) }
.debug_varnames 0 : { *(.debug_varnames) }
/* DWARF 3 */
.debug_pubtypes 0 : { *(.debug_pubtypes) }
.debug_ranges 0 : { *(.debug_ranges) }
/* DWARF Extension. */
.debug_macro 0 : { *(.debug_macro) }
.gnu.attributes 0 : { KEEP (*(.gnu.attributes)) }
/DISCARD/ : { *(.note.GNU-stack) *(.gnu_debuglink) *(.gnu.lto_*)
*(.gnu_object_only) }
}
==================================================
attempt to open
/usr/lib/gcc/x86_64-redhat-linux/4.8.3/../../../../lib64/crt1.o succeeded
/usr/lib/gcc/x86_64-redhat-linux/4.8.3/../../../../lib64/crt1.o
attempt to open
/usr/lib/gcc/x86_64-redhat-linux/4.8.3/../../../../lib64/crti.o succeeded
/usr/lib/gcc/x86_64-redhat-linux/4.8.3/../../../../lib64/crti.o
attempt to open /usr/lib/gcc/x86_64-redhat-linux/4.8.3/crtbegin.o
succeeded
/usr/lib/gcc/x86_64-redhat-linux/4.8.3/crtbegin.o
attempt to open Rmain.o succeeded
Rmain.o
attempt to open /home/jm58660/r-compile-test/sage-6.3/local/lib//libR.so
failed
attempt to open /home/jm58660/r-compile-test/sage-6.3/local/lib//libR.a
failed
attempt to open ../../lib/libR.so succeeded
-lR (../../lib/libR.so)
attempt to open
/home/jm58660/r-compile-test/sage-6.3/local/lib//libgomp.so failed
attempt to open /home/jm58660/r-compile-test/sage-6.3/local/lib//libgomp.a
failed
attempt to open ../../lib/libgomp.so failed
attempt to open ../../lib/libgomp.a failed
attempt to open /usr/lib/gcc/x86_64-redhat-linux/4.8.3/libgomp.so
succeeded
-lgomp (/usr/lib/gcc/x86_64-redhat-linux/4.8.3/libgomp.so)
attempt to open /home/jm58660/r-compile-test/sage-6.3/local/lib//libgcc.so
failed
attempt to open /home/jm58660/r-compile-test/sage-6.3/local/lib//libgcc.a
failed
attempt to open ../../lib/libgcc.so failed
attempt to open ../../lib/libgcc.a failed
attempt to open /usr/lib/gcc/x86_64-redhat-linux/4.8.3/libgcc.so failed
attempt to open /usr/lib/gcc/x86_64-redhat-linux/4.8.3/libgcc.a succeeded
attempt to open
/home/jm58660/r-compile-test/sage-6.3/local/lib//libgcc_s.so failed
attempt to open
/home/jm58660/r-compile-test/sage-6.3/local/lib//libgcc_s.a failed
attempt to open ../../lib/libgcc_s.so failed
attempt to open ../../lib/libgcc_s.a failed
attempt to open /usr/lib/gcc/x86_64-redhat-linux/4.8.3/libgcc_s.so
succeeded
-lgcc_s (/usr/lib/gcc/x86_64-redhat-linux/4.8.3/libgcc_s.so)
attempt to open
/home/jm58660/r-compile-test/sage-6.3/local/lib//libpthread.so failed
attempt to open
/home/jm58660/r-compile-test/sage-6.3/local/lib//libpthread.a failed
attempt to open ../../lib/libpthread.so failed
attempt to open ../../lib/libpthread.a failed
attempt to open /usr/lib/gcc/x86_64-redhat-linux/4.8.3/libpthread.so
failed
attempt to open /usr/lib/gcc/x86_64-redhat-linux/4.8.3/libpthread.a failed
attempt to open
/usr/lib/gcc/x86_64-redhat-linux/4.8.3/../../../../lib64/libpthread.so
succeeded
opened script file
/usr/lib/gcc/x86_64-redhat-linux/4.8.3/../../../../lib64/libpthread.so
opened script file
/usr/lib/gcc/x86_64-redhat-linux/4.8.3/../../../../lib64/libpthread.so
attempt to open /lib64/libpthread.so.0 succeeded
/lib64/libpthread.so.0
attempt to open /usr/lib64/libpthread_nonshared.a succeeded
attempt to open /home/jm58660/r-compile-test/sage-6.3/local/lib//libc.so
failed
attempt to open /home/jm58660/r-compile-test/sage-6.3/local/lib//libc.a
failed
attempt to open ../../lib/libc.so failed
attempt to open ../../lib/libc.a failed
attempt to open /usr/lib/gcc/x86_64-redhat-linux/4.8.3/libc.so failed
attempt to open /usr/lib/gcc/x86_64-redhat-linux/4.8.3/libc.a failed
attempt to open
/usr/lib/gcc/x86_64-redhat-linux/4.8.3/../../../../lib64/libc.so succeeded
opened script file
/usr/lib/gcc/x86_64-redhat-linux/4.8.3/../../../../lib64/libc.so
opened script file
/usr/lib/gcc/x86_64-redhat-linux/4.8.3/../../../../lib64/libc.so
attempt to open /lib64/libc.so.6 succeeded
/lib64/libc.so.6
attempt to open /usr/lib64/libc_nonshared.a succeeded
(/usr/lib64/libc_nonshared.a)elf-init.oS
attempt to open /lib64/ld-linux-x86-64.so.2 succeeded
/lib64/ld-linux-x86-64.so.2
attempt to open /home/jm58660/r-compile-test/sage-6.3/local/lib//libgcc.so
failed
attempt to open /home/jm58660/r-compile-test/sage-6.3/local/lib//libgcc.a
failed
attempt to open ../../lib/libgcc.so failed
attempt to open ../../lib/libgcc.a failed
attempt to open /usr/lib/gcc/x86_64-redhat-linux/4.8.3/libgcc.so failed
attempt to open /usr/lib/gcc/x86_64-redhat-linux/4.8.3/libgcc.a succeeded
attempt to open
/home/jm58660/r-compile-test/sage-6.3/local/lib//libgcc_s.so failed
attempt to open
/home/jm58660/r-compile-test/sage-6.3/local/lib//libgcc_s.a failed
attempt to open ../../lib/libgcc_s.so failed
attempt to open ../../lib/libgcc_s.a failed
attempt to open /usr/lib/gcc/x86_64-redhat-linux/4.8.3/libgcc_s.so
succeeded
-lgcc_s (/usr/lib/gcc/x86_64-redhat-linux/4.8.3/libgcc_s.so)
attempt to open /usr/lib/gcc/x86_64-redhat-linux/4.8.3/crtend.o succeeded
/usr/lib/gcc/x86_64-redhat-linux/4.8.3/crtend.o
attempt to open
/usr/lib/gcc/x86_64-redhat-linux/4.8.3/../../../../lib64/crtn.o succeeded
/usr/lib/gcc/x86_64-redhat-linux/4.8.3/../../../../lib64/crtn.o
libf77blas.so.3 needed by ../../lib/libR.so
libatlas.so.3 needed by ../../lib/libR.so
libgfortran.so.3 needed by ../../lib/libR.so
found libgfortran.so.3 at /usr/local/lib64/libgfortran.so.3
libm.so.6 needed by ../../lib/libR.so
found libm.so.6 at /lib64/libm.so.6
libquadmath.so.0 needed by ../../lib/libR.so
found libquadmath.so.0 at /lib64/libquadmath.so.0
libreadline.so.6 needed by ../../lib/libR.so
found libreadline.so.6 at /lib64/libreadline.so.6
liblzma.so.5 needed by ../../lib/libR.so
found liblzma.so.5 at /lib64/liblzma.so.5
librt.so.1 needed by ../../lib/libR.so
found librt.so.1 at /lib64/librt.so.1
libdl.so.2 needed by ../../lib/libR.so
found libdl.so.2 at /lib64/libdl.so.2
libicuuc.so.50 needed by ../../lib/libR.so
found libicuuc.so.50 at /lib64/libicuuc.so.50
libicui18n.so.50 needed by ../../lib/libR.so
found libicui18n.so.50 at /lib64/libicui18n.so.50
ld-linux-x86-64.so.2 needed by ../../lib/libR.so
found ld-linux-x86-64.so.2 at /lib64/ld-linux-x86-64.so.2
libtinfo.so.5 needed by /lib64/libreadline.so.6
found libtinfo.so.5 at /lib64/libtinfo.so.5
libicudata.so.50 needed by /lib64/libicuuc.so.50
found libicudata.so.50 at /lib64/libicudata.so.50
libstdc++.so.6 needed by /lib64/libicuuc.so.50
found libstdc++.so.6 at /usr/local/lib64/libstdc++.so.6
libgcc_s.so.1 needed by /lib64/libicuuc.so.50
found libgcc_s.so at /usr/lib/gcc/x86_64-redhat-linux/4.8.3/libgcc_s.so
/usr/bin/ld: warning: libf77blas.so.3, needed by ../../lib/libR.so, not
found (try using -rpath or -rpath-link)
/usr/bin/ld: warning: libatlas.so.3, needed by ../../lib/libR.so, not
found (try using -rpath or -rpath-link)
../../lib/libR.so: undefined reference to `drot_'
../../lib/libR.so: undefined reference to `drotg_'
../../lib/libR.so: undefined reference to `dswap_'
../../lib/libR.so: undefined reference to `dgemm_'
../../lib/libR.so: undefined reference to `dnrm2_'
../../lib/libR.so: undefined reference to `dscal_'
../../lib/libR.so: undefined reference to `zgemm_'
../../lib/libR.so: undefined reference to `dtrsm_'
../../lib/libR.so: undefined reference to `daxpy_'
../../lib/libR.so: undefined reference to `dcopy_'
../../lib/libR.so: undefined reference to `dsyrk_'
../../lib/libR.so: undefined reference to `dasum_'
../../lib/libR.so: undefined reference to `ddot_'
collect2: error: ld returned 1 exit status
Furthermore, does
gcc -std=gnu99 -Wl,--export-dynamic -fopenmp
-L/home/jm58660/r-compile-test/sage-6.3/local/lib/ -o R.bin Rmain.o
-L../../lib -lR -lgfortran
work?
No.
/usr/bin/ld: warning: libf77blas.so.3, needed by ../../lib/libR.so, not
found (try using -rpath or -rpath-link)
/usr/bin/ld: warning: libatlas.so.3, needed by ../../lib/libR.so, not
found (try using -rpath or -rpath-link)
../../lib/libR.so: undefined reference to `drot_'
. . .
But in any case, we do not yet know if the problem lies in my setup. Hence
let's wait until I got this tested on clean install. (Which may be next
week.)
--
Jori Mäntysalo
--
You received this message because you are subscribed to the Google Groups
"sage-devel" group.
To unsubscribe from this group and stop receiving emails from it, send an email
to sage-devel+unsubscr...@googlegroups.com.
To post to this group, send email to sage-devel@googlegroups.com.
Visit this group at http://groups.google.com/group/sage-devel.
For more options, visit https://groups.google.com/d/optout.
