Installation issue: gcc@4.8.5

[rountree]

I have successfully installed gcc@develop, gcc@9.2.0 and gcc@9.1.0. gcc@4.8.5 fails.

$ spack install gcc@4.8.5 
...
/mnt/ramdisk/spack/var/spack/stage/rountree/spack-stage-gcc-4.8.5-u2oqtceckujbk3u4tsphayf3mfyboim3/spack-src/spack-build/./gcc/xgcc -B/mnt/ramdisk/spack/var/spack/stage/rountree/spack-stage-gcc-4.8.5-u2oqtceckujbk3u4tsphayf3mfyboim3/spack-src/spack-build/./gcc/ -B/mnt/ramdisk/spack/opt/spack/linux-ubuntu19.10-skylake/gcc-9.2.1/gcc-4.8.5-u2oqtceckujbk3u4tsphayf3mfyboim3/x86_64-unknown-linux-gnu/bin/ -B/mnt/ramdisk/spack/opt/spack/linux-ubuntu19.10-skylake/gcc-9.2.1/gcc-4.8.5-u2oqtceckujbk3u4tsphayf3mfyboim3/x86_64-unknown-linux-gnu/lib/ -isystem /mnt/ramdisk/spack/opt/spack/linux-ubuntu19.10-skylake/gcc-9.2.1/gcc-4.8.5-u2oqtceckujbk3u4tsphayf3mfyboim3/x86_64-unknown-linux-gnu/include -isystem /mnt/ramdisk/spack/opt/spack/linux-ubuntu19.10-skylake/gcc-9.2.1/gcc-4.8.5-u2oqtceckujbk3u4tsphayf3mfyboim3/x86_64-unknown-linux-gnu/sys-include    -g -O2 -O2  -g -O2 -DIN_GCC   -W -Wall -Wno-narrowing -Wwrite-strings -Wcast-qual -Wstrict-prototypes -Wmissing-prototypes -Wold-style-definition  -isystem ./include   -fpic -mlong-double-80 -g -DIN_LIBGCC2 -fbuilding-libgcc -fno-stack-protector   -fpic -mlong-double-80 -I. -I. -I../.././gcc -I/mnt/ramdisk/spack/var/spack/stage/rountree/spack-stage-gcc-4.8.5-u2oqtceckujbk3u4tsphayf3mfyboim3/spack-src/libgcc -I/mnt/ramdisk/spack/var/spack/stage/rountree/spack-stage-gcc-4.8.5-u2oqtceckujbk3u4tsphayf3mfyboim3/spack-src/libgcc/. -I/mnt/ramdisk/spack/var/spack/stage/rountree/spack-stage-gcc-4.8.5-u2oqtceckujbk3u4tsphayf3mfyboim3/spack-src/libgcc/../gcc -I/mnt/ramdisk/spack/var/spack/stage/rountree/spack-stage-gcc-4.8.5-u2oqtceckujbk3u4tsphayf3mfyboim3/spack-src/libgcc/../include -I/mnt/ramdisk/spack/var/spack/stage/rountree/spack-stage-gcc-4.8.5-u2oqtceckujbk3u4tsphayf3mfyboim3/spack-src/libgcc/config/libbid -DENABLE_DECIMAL_BID_FORMAT -DHAVE_CC_TLS  -DUSE_TLS -o emutls.o -MT emutls.o -MD -MP -MF emutls.dep -fexceptions -c /mnt/ramdisk/spack/var/spack/stage/rountree/spack-stage-gcc-4.8.5-u2oqtceckujbk3u4tsphayf3mfyboim3/spack-src/libgcc/emutls.c -fvisibility=hidden -DHIDE_EXPORTS
In file included from /mnt/ramdisk/spack/var/spack/stage/rountree/spack-stage-gcc-4.8.5-u2oqtceckujbk3u4tsphayf3mfyboim3/spack-src/libgcc/unwind-dw2.c:405:0:
./md-unwind-support.h: In function 'x86_64_fallback_frame_state':
./md-unwind-support.h:65:47: error: dereferencing pointer to incomplete type
       sc = (struct sigcontext *) (void *) &uc_->uc_mcontext;
                                               ^

A similar issue was reported against gcc here with fixes backported to gcc-7.1.1, gcc-6.5.0 and gcc-5.5.0.

A similar Issue also reported here: stackoverflow with the following diagnosis from Johnathan Wakely (not quite on point):

N.B. the problem has nothing to do with using GCC 7.2, it's caused by the recent version of glibc used by your Arch system. Glibc headers stopped declaring the non-standard name struct ucontext and now only use the ucontext_t typedef required by POSIX.

The version of xgcc used above is, of course, 4.8.5. However...

$ ldd /mnt/ramdisk/spack/var/spack/stage/rountree/spack-stage-gcc-4.8.5-u2oqtceckujbk3u4tsphayf3mfyboim3/spack-src/spack-build/./gcc/xgcc 
	linux-vdso.so.1 (0x00007ffc151ff000)
	libiconv.so.2 => /mnt/ramdisk/spack/opt/spack/linux-ubuntu19.10-skylake/gcc-9.2.1/libiconv-1.16-pauu3o43t7lav57d3zwjw5ze5uh6yek2/lib/libiconv.so.2 (0x00007f0aa285b000)
	libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f0aa264f000)
	/lib64/ld-linux-x86-64.so.2 (0x00007f0aa2a58000)

I'm guessing that libc-6.0 is too new to build the ancient gcc-4.8.5, but I'm new enough to spack that I don't know how to go about forcing and older version of the library to be used instead.

A few other notes:

$ uname -a 
Linux Solvent 5.3.0-40-generic #32-Ubuntu SMP Fri Jan 31 20:24:34 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux
$ lsb_release -d
Description:	Ubuntu 19.10

packages.yaml compilers.yaml are both unchanged from stock.

$ spack spec --install-status gcc@4.8.5
Input spec
--------------------------------
 -   gcc@4.8.5

Concretized
--------------------------------
 -   gcc@4.8.5%gcc@9.2.1~binutils languages=c,c++,fortran ~nvptx patches=0689c26bd7f38c5c9594eb8a4932ae7fce96cc8796c45839e050dc42c83112f1 ~piclibs~strip arch=linux-ubuntu19.10-skylake
[+]      ^gmp@6.1.2%gcc@9.2.1 arch=linux-ubuntu19.10-skylake
[+]          ^autoconf@2.69%gcc@9.2.1 arch=linux-ubuntu19.10-skylake
[+]              ^m4@1.4.18%gcc@9.2.1 patches=3877ab548f88597ab2327a2230ee048d2d07ace1062efe81fc92e91b7f39cd00,fc9b61654a3ba1a8d6cd78ce087e7c96366c290bc8d2c299f09828d793b853c8 +sigsegv arch=linux-ubuntu19.10-skylake
[+]                  ^libsigsegv@2.12%gcc@9.2.1 arch=linux-ubuntu19.10-skylake
[+]              ^perl@5.30.0%gcc@9.2.1+cpanm+shared+threads arch=linux-ubuntu19.10-skylake
[+]                  ^gdbm@1.18.1%gcc@9.2.1 arch=linux-ubuntu19.10-skylake
[+]                      ^readline@8.0%gcc@9.2.1 arch=linux-ubuntu19.10-skylake
[+]                          ^ncurses@6.1%gcc@9.2.1~symlinks~termlib arch=linux-ubuntu19.10-skylake
[+]                              ^pkgconf@1.6.3%gcc@9.2.1 arch=linux-ubuntu19.10-skylake
[+]          ^automake@1.16.1%gcc@9.2.1 arch=linux-ubuntu19.10-skylake
[+]          ^libtool@2.4.6%gcc@9.2.1 arch=linux-ubuntu19.10-skylake
[+]      ^libiconv@1.16%gcc@9.2.1 arch=linux-ubuntu19.10-skylake
[+]      ^mpc@1.1.0%gcc@9.2.1 arch=linux-ubuntu19.10-skylake
[+]          ^mpfr@3.1.6%gcc@9.2.1 patches=66a5d58364113a21405fc53f4a48f4e8 arch=linux-ubuntu19.10-skylake

[romintomasetti]

Step 0

I tested in a fresh Ubuntu 20 docker image (installing gcc g++ gfortran make curl)

* **Spack:** 0.16.1-2184-6c632dad71
* **Python:** 3.8.5
* **Platform:** linux-ubuntu20.04-skylake
* **Concretizer:** original

Step 1

• spack install gcc@4.8.5 ends up in the error mentioned above.

Step 2

• Apply the patch found in https://gcc.gnu.org/git/?p=gcc.git&a=commit;h=16b277761b432510ad6dcf72d877ae72b5f0a4b7, mentioned by @rountree .

  • adding patch('custom.patch',when='@4.8.5 os=ubuntu20.04') to the ../repos/builtin/packages/gcc/packages.py
  • patch file : custom.patch.txt

• spack install gcc@4.8.5 ends up in

     29738    echo INHIBIT_LIBC_CFLAGS = '' >> tmp-libgcc.mvars
  >> 29739    xgcc: error trying to exec 'cc1': execvp: No such file or directory
     29740    echo TARGET_SYSTEM_ROOT = '' >> tmp-libgcc.mvars

Here is the full log:
spack-build-out.txt

Note This patch is already in spack under ucontext_t.patch.

Step 3

I tried to make it with a single thread (-j1) and the error is

     31845    checking for a thread-safe mkdir -p... /usr/bin/mkdir -p
     31846    checking for gawk... mawk
     31847    checking whether make sets $(MAKE)... yes
     31848    checking whether to enable maintainer-specific portions of Makefiles... no
     31849    checking for x86_64-unknown-linux-gnu-gcc... /tmp/root/spack-stage/spack-stage-gcc-4.8.5-4uzyfcq4bzbt3txtvwqflmtiyft2
              nbn6/spack-src/spack-build/./gcc/xgcc -B/tmp/root/spack-stage/spack-stage-gcc-4.8.5-4uzyfcq4bzbt3txtvwqflmtiyft2nbn6/
              spack-src/spack-build/./gcc/ -B/spack/opt/spack/linux-ubuntu20.04-skylake/gcc-9.3.0/gcc-4.8.5-4uzyfcq4bzbt3txtvwqflmt
              iyft2nbn6/x86_64-unknown-linux-gnu/bin/ -B/spack/opt/spack/linux-ubuntu20.04-skylake/gcc-9.3.0/gcc-4.8.5-4uzyfcq4bzbt
              3txtvwqflmtiyft2nbn6/x86_64-unknown-linux-gnu/lib/ -isystem /spack/opt/spack/linux-ubuntu20.04-skylake/gcc-9.3.0/gcc-
              4.8.5-4uzyfcq4bzbt3txtvwqflmtiyft2nbn6/x86_64-unknown-linux-gnu/include -isystem /spack/opt/spack/linux-ubuntu20.04-s
              kylake/gcc-9.3.0/gcc-4.8.5-4uzyfcq4bzbt3txtvwqflmtiyft2nbn6/x86_64-unknown-linux-gnu/sys-include
     31850    checking for C compiler default output file name...
  >> 31851    configure: error: in `/tmp/root/spack-stage/spack-stage-gcc-4.8.5-4uzyfcq4bzbt3txtvwqflmtiyft2nbn6/spack-src/spack-bu
              ild/x86_64-unknown-linux-gnu/libsanitizer':
  >> 31852    configure: error: C compiler cannot create executables
     31853    See `config.log' for more details.
     31854    make[2]: *** [Makefile:13896: configure-stage1-target-libsanitizer] Error 77
     31855    make[2]: Leaving directory '/tmp/root/spack-stage/spack-stage-gcc-4.8.5-4uzyfcq4bzbt3txtvwqflmtiyft2nbn6/spack-src/sp
              ack-build'
     31856    make[1]: *** [Makefile:19785: stage1-bubble] Error 2
     31857    make[1]: Leaving directory '/tmp/root/spack-stage/spack-stage-gcc-4.8.5-4uzyfcq4bzbt3txtvwqflmtiyft2nbn6/spack-src/sp
              ack-build'
     31858    make: *** [Makefile:886: all] Error 2

Here is the config.log from /tmp/root/spack-stage/spack-stage-gcc-4.8.5-4uzyfcq4bzbt3txtvwqflmtiyft2nbn6/spack-src/spack-build/x86_64-unknown-linux-gnu/libsanitizer/
config.log
and a relevant extract from this file is

/tmp/root/spack-stage/spack-stage-gcc-4.8.5-4uzyfcq4bzbt3txtvwqflmtiyft2nbn6/spack-src/spack-build/./gcc/cc1: /tmp/root/spack-stage/spack-stage-gcc-4.8.5-4uzyfcq4bzbt3txtvwqflmtiyft2nbn6/spack-src/spack-build/x86_64-unknown-linux-gnu/libstdc++-v3/src/.libs/libstdc++.so.6: version `CXXABI_1.3.9' not found (required by /tmp/root/spack-stage/spack-stage-gcc-4.8.5-4uzyfcq4bzbt3txtvwqflmtiyft2nbn6/spack-src/spack-build/./gcc/cc1)

which is awaited as

strings /tmp/root/spack-stage/spack-stage-gcc-4.8.5-4uzyfcq4bzbt3txtvwqflmtiyft2nbn6/spack-src/spack-build/x86_64-unknown-linux-gnu/libstdc++-v3/src/.libs/libstdc++.so.6 | grep CXXABI
CXXABI_1.3
CXXABI_1.3.1
CXXABI_1.3.2
CXXABI_1.3.3
CXXABI_1.3.4
CXXABI_1.3.5
CXXABI_1.3.6
CXXABI_1.3.7
CXXABI_TM_1
CXXABI_1.3
CXXABI_1.3.2
CXXABI_1.3.6
CXXABI_1.3.1
CXXABI_1.3.5
CXXABI_1.3.4
CXXABI_TM_1
CXXABI_1.3.7
CXXABI_1.3.3

this ABI is indeed not present.

Step 4

So I've tried preloading as suggested in https://hpc-discourse.usc.edu/t/usr-lib64-libstdc-so-6-too-old/171/4:

root@93c78c74120b:/spack# LD_PRELOAD=/usr/lib/x86_64-linux-gnu/libstdc++.so.6 ./bin/spack install -v -j1 gcc@4.8.5

but it failed with

32091    /tmp/root/spack-stage/spack-stage-gcc-4.8.5-4uzyfcq4bzbt3txtvwqflmtiyft2nbn6/spack-src/libsanitizer/asan/asan_linux.cc: In function 'bool __asan::AsanInterceptsSignal(int)':
  >> 32092    /tmp/root/spack-stage/spack-stage-gcc-4.8.5-4uzyfcq4bzbt3txtvwqflmtiyft2nbn6/spack-src/libsanitizer/asan/asan_linux.cc:95:20: error: 'SIGSEGV' was not declared in this scope
     32093       return signum == SIGSEGV && flags()->handle_segv;
     32094                        ^
     32095    /tmp/root/spack-stage/spack-stage-gcc-4.8.5-4uzyfcq4bzbt3txtvwqflmtiyft2nbn6/spack-src/libsanitizer/asan/asan_linux.cc:96:1: warning: control reaches end of non-void function [-Wreturn-typ
              e]
     32096     }
     32097     ^
     32098    make[4]: *** [Makefile:441: asan_linux.lo] Error 1

so I'll try the patch suggested in https://patchwork.ozlabs.org/project/gcc/patch/6824253.3U2boEivI2@devpool21/.

Note In fact this patch is already in spack under signal.patch.

Step 5

I applied the patch https://patchwork.ozlabs.org/project/gcc/patch/6824253.3U2boEivI2@devpool21/ and again it failed

32171    /tmp/root/spack-stage/spack-stage-gcc-4.8.5-n4s2pbg3distxn6uzewvzqf3eck7x2su/spack-src/libsanitizer/tsan/tsan_platform_linux.cc: In function 'int __tsan::ExtractResolvFDs(void*, int*, int)
              ':
  >> 32172    /tmp/root/spack-stage/spack-stage-gcc-4.8.5-n4s2pbg3distxn6uzewvzqf3eck7x2su/spack-src/libsanitizer/tsan/tsan_platform_linux.cc:295:16: error: 'statp' was not declared in this scope
     32173       __res_state *statp = (__res_state*)state;
     32174                    ^
  >> 32175    /tmp/root/spack-stage/spack-stage-gcc-4.8.5-n4s2pbg3distxn6uzewvzqf3eck7x2su/spack-src/libsanitizer/tsan/tsan_platform_linux.cc:295:37: error: expected primary-expression before ')' token
     32176       __res_state *statp = (__res_state*)state;
     32177                                         ^
  >> 32178    /tmp/root/spack-stage/spack-stage-gcc-4.8.5-n4s2pbg3distxn6uzewvzqf3eck7x2su/spack-src/libsanitizer/tsan/tsan_platform_linux.cc:295:38: error: expected ';' before 'state'
     32179       __res_state *statp = (__res_state*)state;
     32180                                          ^
     32181    make[4]: *** [Makefile:475: tsan_platform_linux.lo] Error 1

Successful step

In the end, starting from scratch:

• package.py modified to add:

    patch('ucontext_t-4.8.patch',when='@4.8.5 os=ubuntu20.04')
    patch('signal.patch',when='@4.8.5 os=ubuntu20.04')
    patch('stack_t-4.8.patch', when='@4.8 os=ubuntu20.04')

• patches (just taking the patches already in spack and removing what should not be there)
  stack_t-4.8.patch.txt
  ucontext_t-4.8.patch.txt

It works only with the preload:

LD_PRELOAD=/usr/lib/x86_64-linux-gnu/libstdc++.so.6 spack install gcc@4.8.5