GROMACS version:2024.1
GROMACS modification: No
Here post your question:
Hi, I am trying to build gromacs with the following command :
spack install gromacs@2024.1%oneapi@2023.2.0 +sycl +mpi
[+] /lustre/home/br-kolgu/spack/opt/spack/linux-rhel8-zen3/gcc-12.2.0/nghttp2-1.57.0-54czeqmr4qadkqnnuuzufd2p4aohmqla
[+] /lustre/home/br-kolgu/spack/opt/spack/linux-rhel8-zen3/gcc-12.2.0/zlib-ng-2.1.4-bjplwahje7noykqhjer44gvw6lxxxu6a
[+] /lustre/home/br-kolgu/spack/opt/spack/linux-rhel8-zen3/gcc-12.2.0/gcc-runtime-12.2.0-muur22hgsecvh3dmnxoj7pjnh3teddgt
[+] /lustre/home/br-kolgu/spack/opt/spack/linux-rhel8-zen3/gcc-12.2.0/ncurses-6.4-latmykf333bg4koph5oisuf5x2ykcuup
[+] /lustre/home/br-kolgu/spack/opt/spack/linux-rhel8-zen3/gcc-12.2.0/libpciaccess-0.17-pmhly5zyy6wqkto2jln4yfp7mvanmkol
[+] /lustre/home/br-kolgu/spack/opt/spack/linux-rhel8-zen3/gcc-12.2.0/libiconv-1.17-4ojv6rziro46rpde5sgportja7pnblxn
[+] /lustre/home/br-kolgu/spack/opt/spack/linux-rhel8-zen3/gcc-12.2.0/xz-5.4.1-jkitpb4skhoxz2acotalylot7n366ouk
[+] /lustre/home/br-kolgu/spack/opt/spack/linux-rhel8-zen3/gcc-12.2.0/bzip2-1.0.8-fv7pkikc4iv3sxwnf4eqwnjeynmpad5p
[+] /lustre/home/br-kolgu/spack/opt/spack/linux-rhel8-zen3/gcc-12.2.0/zstd-1.5.5-xygti2fgvunhsafaejcsgtar76ex4u27
[+] /lustre/home/br-kolgu/spack/opt/spack/linux-rhel8-zen3/gcc-12.2.0/libxcrypt-4.4.35-pr64fai4gsx435qcwymvtrhb6tdetnll
[+] /lustre/home/br-kolgu/spack/opt/spack/linux-rhel8-zen3/gcc-12.2.0/libsigsegv-2.14-ybxkihunotlqrc6geedhwbwbemstmzv5
[+] /lustre/home/br-kolgu/spack/opt/spack/linux-rhel8-zen3/gcc-12.2.0/libtool-2.4.7-uttansg3nmrjf47ak2iyyeem4vj7ovtc
[+] /lustre/home/br-kolgu/spack/opt/spack/linux-rhel8-zen3/gcc-12.2.0/berkeley-db-18.1.40-5fg7mbulac7qu4rtqkxb3mi2zddd2zkx
[+] /lustre/home/br-kolgu/spack/opt/spack/linux-rhel8-zen3/gcc-12.2.0/pkgconf-1.9.5-ul6hjnq6oyu23adcckiq7mxvbgqjbrkr
[+] /lustre/home/br-kolgu/spack/opt/spack/linux-rhel8-zen3/gcc-12.2.0/pigz-2.7-xuu6ppgnylbnlryixsdfwoqzm7lyv6wg
[+] /lustre/home/br-kolgu/spack/opt/spack/linux-rhel8-zen3/gcc-12.2.0/openssl-3.1.3-s5lnl2zhthvjtjilifmhx77wo5ckex5x
[+] /lustre/home/br-kolgu/spack/opt/spack/linux-rhel8-zen3/oneapi-2023.2.0/intel-oneapi-runtime-2023.2.0-2ah3tk6qdovkuusve7w2flnyk3hwgxzv
[+] /lustre/home/br-kolgu/spack/opt/spack/linux-rhel8-zen3/gcc-12.2.0/openblas-0.3.26-y3zkkqimtkqvwmj3tlnunpgop2efoep4
[+] /lustre/home/br-kolgu/spack/opt/spack/linux-rhel8-zen3/gcc-12.2.0/gmake-4.4.1-ajgjo2s5vzg3cblmtl426pvsv6hpewpe
[+] /lustre/home/br-kolgu/spack/opt/spack/linux-rhel8-zen3/gcc-12.2.0/readline-8.2-dguilf37kabiqbw7csgwdoyajkmxna4e
[+] /lustre/home/br-kolgu/spack/opt/spack/linux-rhel8-zen3/gcc-12.2.0/diffutils-3.9-q2t5dyyjqc34dclnyfetvynuyd3godsj
[+] /lustre/home/br-kolgu/spack/opt/spack/linux-rhel8-zen3/gcc-12.2.0/numactl-2.0.14-f5ihi6yu6p7an2y66gl5aw5xmigwkbur
[+] /lustre/home/br-kolgu/spack/opt/spack/linux-rhel8-zen3/gcc-12.2.0/libxml2-2.10.3-j5a3gl4ejwz7l4xal76yektiiondt7qa
[+] /lustre/home/br-kolgu/spack/opt/spack/linux-rhel8-zen3/gcc-12.2.0/libedit-3.1-20210216-jr5sxzej33d7mxxmdwmojg2ascvu6wtq
[+] /lustre/home/br-kolgu/spack/opt/spack/linux-rhel8-zen3/gcc-12.2.0/tar-1.34-jk4m7s6kogjvthumdoa2sreglwg3eky5
[+] /lustre/home/br-kolgu/spack/opt/spack/linux-rhel8-zen3/gcc-12.2.0/curl-8.4.0-3ulpttd4cqk6fkhq4ol35eh7pc6slozm
[+] /lustre/home/br-kolgu/spack/opt/spack/linux-rhel8-zen3/oneapi-2023.2.0/gmp-6.2.1-xqtfzsqghtap6ym6rbhs52ms4kio27h2
[+] /lustre/home/br-kolgu/spack/opt/spack/linux-rhel8-zen3/gcc-12.2.0/libevent-2.1.12-a4q5pxzgoq6gnmwucyoxq65b54dzm5rr
[+] /lustre/home/br-kolgu/spack/opt/spack/linux-rhel8-zen3/gcc-12.2.0/gdbm-1.23-nrftdj2zmebq2zutsydwaapg4btwmdof
[+] /lustre/home/br-kolgu/spack/opt/spack/linux-rhel8-zen3/gcc-12.2.0/hwloc-2.9.1-mfzirwqcuqrsbhpy6llgnshll6fayibp
[+] /lustre/home/br-kolgu/spack/opt/spack/linux-rhel8-zen3/gcc-12.2.0/gettext-0.22.3-2lc42wsvykrc4ouwqla6gq3xzyofcyjr
[+] /lustre/home/br-kolgu/spack/opt/spack/linux-rhel8-zen3/gcc-12.2.0/cmake-3.26.6-iobnbee5qe6uduthgern7qomo4gv4sro
[+] /lustre/home/br-kolgu/spack/opt/spack/linux-rhel8-zen3/oneapi-2023.2.0/mpfr-3.1.6-anhwwubuf4mfinnkajgado3rqvsyo7tn
[+] /lustre/home/br-kolgu/spack/opt/spack/linux-rhel8-zen3/gcc-12.2.0/perl-5.38.0-ebchflxbysacgyfjzx2apheukjpbwanp
[+] /lustre/home/br-kolgu/spack/opt/spack/linux-rhel8-zen3/gcc-12.2.0/pmix-5.0.1-ktrmmztxcxt2k5fnhprgkffmcmzzvugs
[+] /lustre/home/br-kolgu/spack/opt/spack/linux-rhel8-zen3/oneapi-2023.2.0/gawk-5.3.0-npui33ruc23fioxfd3qgmimuafhxzodh
[+] /lustre/home/br-kolgu/spack/opt/spack/linux-rhel8-zen3/oneapi-2023.2.0/mpc-1.1.0-vnkm4h4zbucrc6z6apuuittotjziy3ny
[+] /lustre/home/br-kolgu/spack/opt/spack/linux-rhel8-zen3/gcc-12.2.0/krb5-1.20.1-egezrbvhih2s6gghdfv2odngl2p4uts7
[+] /lustre/home/br-kolgu/spack/opt/spack/linux-rhel8-zen3/oneapi-2023.2.0/texinfo-7.0.3-4tcwh4aakq3344a4sbkkm57x2ut6dpry
[+] /lustre/home/br-kolgu/spack/opt/spack/linux-rhel8-zen3/gcc-12.2.0/openssh-9.5p1-7ftfdac4lips6jjtkubihdrv62svwwns
==> Installing gcc-9.5.0-j6k37tfsrtg5ikwz5ifun2rso6vpuu2w [41/44]
==> No binary for gcc-9.5.0-j6k37tfsrtg5ikwz5ifun2rso6vpuu2w found: installing from source
==> Using cached archive: /lustre/home/br-kolgu/spack/var/spack/cache/_source-cache/archive/27/27769f64ef1d4cd5e2be8682c0c93f9887983e6cfd1a927ce5a0a2915a95cf8f.tar.xz
==> Using cached archive: /lustre/home/br-kolgu/spack/var/spack/cache/_source-cache/archive/0d/0d136226eb07bc43f1b15284f48bd252e3748a0426b5d7ac9084ebc406e15490
==> Applied patch /lustre/home/br-kolgu/spack/var/spack/repos/builtin/packages/gcc/glibc-2.36-libsanitizer-gcc-5-9.patch
==> Applied patch https://github.com/gcc-mirror/gcc/commit/423cd47cfc9640ba3d6811b780e8a0b94b704dcb.patch?full_index=1
==> Ran patch() for gcc
==> gcc: Executing phase: 'autoreconf'
==> gcc: Executing phase: 'configure'
==> gcc: Executing phase: 'build'
==> Error: ProcessError: Command exited with status 2:
'make' '-j16' 'V=1'
13 errors found in build log:
11890 #define offsetof(t, d) __builtin_offsetof(t, d)
11891 ^ ~
11892 In file included from /tmp/br-kolgu/spack-stage/spack-stage-gcc-9.5.0-j6k37tfsrtg5ikwz5ifun2rso6vpuu2w/spack-src/gcc/rtl.c:131:
11893 /tmp/br-kolgu/spack-stage/spack-stage-gcc-9.5.0-j6k37tfsrtg5ikwz5ifun2rso6vpuu2w/spack-src/gcc/rtl.def:974:1: warning: offset of on non-POD type 'struct rtx_def' [-Winvalid-offse
tof]
11894 DEF_RTL_EXPR(DEFINE_ASM_ATTRIBUTES, "define_asm_attributes", "V", RTX_EXTRA)
11895 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>> 11896 /tmp/br-kolgu/spack-stage/spack-stage-gcc-9.5.0-j6k37tfsrtg5ikwz5ifun2rso6vpuu2w/spack-src/gcc/rtl.c:128:6: /lustre/home/br-kolgu/spack/lib/spack/env/oneapi/icpx -std=gnu++98 -c
-g -O1 -DIN_GCC -fno-strict-aliasing -fno-exceptions -fno-rtti -fasynchronous-unwind-tables -W -Wall -Wno-narrowing -Wwrite-strings -Wcast-qual -Wno-format -Wmissing-format-
attribute -Woverloaded-virtual -pedantic -Wno-long-long -Wno-variadic-macros -Wno-overlength-strings -fno-common -DHAVE_CONFIG_H -DGENERATOR_FILE -fno-PIE -I. -Ibuild -I/tmp/br
-kolgu/spack-stage/spack-stage-gcc-9.5.0-j6k37tfsrtg5ikwz5ifun2rso6vpuu2w/spack-src/gcc -I/tmp/br-kolgu/spack-stage/spack-stage-gcc-9.5.0-j6k37tfsrtg5ikwz5ifun2rso6vpuu2w/spack-s
rc/gcc/build -I/tmp/br-kolgu/spack-stage/spack-stage-gcc-9.5.0-j6k37tfsrtg5ikwz5ifun2rso6vpuu2w/spack-src/gcc/../include -I/tmp/br-kolgu/spack-stage/spack-stage-gcc-9.5.0-j6k37t
fsrtg5ikwz5ifun2rso6vpuu2w/spack-src/gcc/../libcpp/include \
11897 -o build/hash-table.o /tmp/br-kolgu/spack-stage/spack-stage-gcc-9.5.0-j6k37tfsrtg5ikwz5ifun2rso6vpuu2w/spack-src/gcc/hash-table.c
11898 note: expanded from macro 'DEF_RTL_EXPR'
11899 ? RTX_HDR_SIZE + sizeof (reg_info) \
11900 ^~~~~~~~~~~~
11901 /tmp/br-kolgu/spack-stage/spack-stage-gcc-9.5.0-j6k37tfsrtg5ikwz5ifun2rso6vpuu2w/spack-src/gcc/rtl.h:694:22: note: expanded from macro 'RTX_HDR_SIZE'
11902 #define RTX_HDR_SIZE offsetof (struct rtx_def, u)
...
13646 In file included from /tmp/br-kolgu/spack-stage/spack-stage-gcc-9.5.0-j6k37tfsrtg5ikwz5ifun2rso6vpuu2w/spack-src/gcc/genattr.c:26:
13647 In file included from /tmp/br-kolgu/spack-stage/spack-stage-gcc-9.5.0-j6k37tfsrtg5ikwz5ifun2rso6vpuu2w/spack-src/gcc/rtl.h:31:
13648 In file included from /tmp/br-kolgu/spack-stage/spack-stage-gcc-9.5.0-j6k37tfsrtg5ikwz5ifun2rso6vpuu2w/spack-src/gcc/hash-table.h:575:
13649 /tmp/br-kolgu/spack-stage/spack-stage-gcc-9.5.0-j6k37tfsrtg5ikwz5ifun2rso6vpuu2w/spack-src/gcc/mem-stats.h:126:1: warning: 'mem_usage' defined as a struct here but previously dec
lared as a class; this is valid, but may result in linker errors under the Microsoft C++ ABI [-Wmismatched-tags]
13650 struct mem_usage
13651 ^
>> 13652 /tmp/br-kolgu/spack-stage/spack-stage-gcc-9.5.0-j6k37tfsrtg5ikwz5ifun2rso6vpuu2w/spack-src/gcc/hash-table.h:350:1: /tmp/br-kolgu/spack-stage/spack-stage-gcc-9.5.0-j6k37tfsrtg5ikw
z5ifun2rso6vpuu2w/spack-src/gcc/hash-table.hnote: :did you mean struct here?350
13653 :1: note: did you mean struct here?
13654 class mem_usage;
13655 ^~~~~
13656 struct
13657 class mem_usage;
13658 ^~~~~
...
13975 build/genpreds /tmp/br-kolgu/spack-stage/spack-stage-gcc-9.5.0-j6k37tfsrtg5ikwz5ifun2rso6vpuu2w/spack-src/gcc/common.md /tmp/br-kolgu/spack-stage/spack-stage-gcc-9.5.0-j6k37tfsrt
g5ikwz5ifun2rso6vpuu2w/spack-src/gcc/config/i386/i386.md > tmp-preds.c
13976 build/genpreds -h /tmp/br-kolgu/spack-stage/spack-stage-gcc-9.5.0-j6k37tfsrtg5ikwz5ifun2rso6vpuu2w/spack-src/gcc/common.md /tmp/br-kolgu/spack-stage/spack-stage-gcc-9.5.0-j6k37tf
srtg5ikwz5ifun2rso6vpuu2w/spack-src/gcc/config/i386/i386.md > tmp-preds.h
13977 build/genconditions /tmp/br-kolgu/spack-stage/spack-stage-gcc-9.5.0-j6k37tfsrtg5ikwz5ifun2rso6vpuu2w/spack-src/gcc/common.md /tmp/br-kolgu/spack-stage/spack-stage-gcc-9.5.0-j6k37
tfsrtg5ikwz5ifun2rso6vpuu2w/spack-src/gcc/config/i386/i386.md > tmp-condmd.c
13978 build/genpreds -c /tmp/br-kolgu/spack-stage/spack-stage-gcc-9.5.0-j6k37tfsrtg5ikwz5ifun2rso6vpuu2w/spack-src/gcc/common.md /tmp/br-kolgu/spack-stage/spack-stage-gcc-9.5.0-j6k37tf
srtg5ikwz5ifun2rso6vpuu2w/spack-src/gcc/config/i386/i386.md > tmp-constrs.h
13979 /lustre/home/br-kolgu/spack/lib/spack/env/oneapi/icpx -std=gnu++98 -g -O1 -DIN_GCC -fno-strict-aliasing -fno-exceptions -fno-rtti -fasynchronous-unwind-tables -W -Wall -Wno-
narrowing -Wwrite-strings -Wcast-qual -Wno-format -Wmissing-format-attribute -Woverloaded-virtual -pedantic -Wno-long-long -Wno-variadic-macros -Wno-overlength-strings -fno-commo
n -DHAVE_CONFIG_H -DGENERATOR_FILE -fno-PIE -Wl,-rpath,/lustre/home/br-kolgu/spack/opt/spack/linux-rhel8-zen3/oneapi-2023.2.0/gcc-9.5.0-j6k37tfsrtg5ikwz5ifun2rso6vpuu2w/lib -Wl
,-rpath,/lustre/home/br-kolgu/spack/opt/spack/linux-rhel8-zen3/oneapi-2023.2.0/gcc-9.5.0-j6k37tfsrtg5ikwz5ifun2rso6vpuu2w/lib64 -Wl,-rpath,/lustre/home/br-kolgu/spack/opt/spack/l
inux-rhel8-zen3/oneapi-2023.2.0/gmp-6.2.1-xqtfzsqghtap6ym6rbhs52ms4kio27h2/lib -Wl,-rpath,/lustre/home/br-kolgu/spack/opt/spack/linux-rhel8-zen3/oneapi-2023.2.0/intel-oneapi-runt
ime-2023.2.0-2ah3tk6qdovkuusve7w2flnyk3hwgxzv/lib -Wl,-rpath,/lustre/home/br-kolgu/spack/opt/spack/linux-rhel8-zen3/oneapi-2023.2.0/mpc-1.1.0-vnkm4h4zbucrc6z6apuuittotjziy3ny/lib
-Wl,-rpath,/lustre/home/br-kolgu/spack/opt/spack/linux-rhel8-zen3/oneapi-2023.2.0/mpfr-3.1.6-anhwwubuf4mfinnkajgado3rqvsyo7tn/lib -Wl,-rpath,/lustre/home/br-kolgu/spack/opt/spac
k/linux-rhel8-zen3/gcc-12.2.0/zlib-ng-2.1.4-bjplwahje7noykqhjer44gvw6lxxxu6a/lib -no-pie -o build/genattrtab \
13980 build/genattrtab.o build/rtl.o build/read-rtl.o build/ggc-none.o build/vec.o build/min-insn-modes.o build/gensupport.o build/print-rtl.o build/hash-table.o build/sort.o build
/read-md.o build/errors.o ../build-x86_64-pc-linux-gnu/libiberty/libiberty.a
>> 13981 /tmp/br-kolgu/spack-stage/spack-stage-gcc-9.5.0-j6k37tfsrtg5ikwz5ifun2rso6vpuu2w/spack-src/gcc/config/i386/sse.md:18340:26: error: '@@' used without iterators
13982 /tmp/br-kolgu/spack-stage/spack-stage-gcc-9.5.0-j6k37tfsrtg5ikwz5ifun2rso6vpuu2w/spack-src/gcc/config/i386/sse.md:18340:27: note: following context is `)'
>> 13983 make[3]: *** [Makefile:2423: s-preds] Error 1
13984 make[3]: *** Waiting for unfinished jobs....
>> 13985 /tmp/br-kolgu/spack-stage/spack-stage-gcc-9.5.0-j6k37tfsrtg5ikwz5ifun2rso6vpuu2w/spack-src/gcc/config/i386/sse.md:18340:26: error: '@@' used without iterators
13986 /tmp/br-kolgu/spack-stage/spack-stage-gcc-9.5.0-j6k37tfsrtg5ikwz5ifun2rso6vpuu2w/spack-src/gcc/config/i386/sse.md:18340:27: note: following context is `)'
>> 13987 /tmp/br-kolgu/spack-stage/spack-stage-gcc-9.5.0-j6k37tfsrtg5ikwz5ifun2rso6vpuu2w/spack-src/gcc/config/i386/sse.md:18340:26: error: '@@' used without iterators
13988 /tmp/br-kolgu/spack-stage/spack-stage-gcc-9.5.0-j6k37tfsrtg5ikwz5ifun2rso6vpuu2w/spack-src/gcc/config/i386/sse.md:18340:27: note: following context is `)'
>> 13989 make[3]: *** [Makefile:2428: s-preds-h] Error 1
>> 13990 make[3]: *** [Makefile:2433: s-constrs-h] Error 1
>> 13991 /tmp/br-kolgu/spack-stage/spack-stage-gcc-9.5.0-j6k37tfsrtg5ikwz5ifun2rso6vpuu2w/spack-src/gcc/config/i386/sse.md:18340:26: error: '@@' used without iterators
13992 /tmp/br-kolgu/spack-stage/spack-stage-gcc-9.5.0-j6k37tfsrtg5ikwz5ifun2rso6vpuu2w/spack-src/gcc/config/i386/sse.md:18340:27: note: following context is `)'
>> 13993 make[3]: *** [Makefile:2367: s-conditions] Error 1
13994 10 warnings generated.
13995 16 warnings generated.
13996 7 warnings generated.
13997 rm gcc.pod
13998 make[3]: Leaving directory '/tmp/br-kolgu/spack-stage/spack-stage-gcc-9.5.0-j6k37tfsrtg5ikwz5ifun2rso6vpuu2w/spack-src/spack-build/gcc'
>> 13999 make[2]: *** [Makefile:4667: all-stage1-gcc] Error 2
14000 make[2]: Leaving directory '/tmp/br-kolgu/spack-stage/spack-stage-gcc-9.5.0-j6k37tfsrtg5ikwz5ifun2rso6vpuu2w/spack-src/spack-build'
>> 14001 make[1]: *** [Makefile:22823: stage1-bubble] Error 2
14002 make[1]: Leaving directory '/tmp/br-kolgu/spack-stage/spack-stage-gcc-9.5.0-j6k37tfsrtg5ikwz5ifun2rso6vpuu2w/spack-src/spack-build'
>> 14003 make: *** [Makefile:994: all] Error 2
See build log for details:
/tmp/br-kolgu/spack-stage/spack-stage-gcc-9.5.0-j6k37tfsrtg5ikwz5ifun2rso6vpuu2w/spack-build-out.txt
==> Warning: Skipping build of gromacs-2024.1-qvl47qjtobwiekrtnuryfi3dug3fj7tp since gcc-9.5.0-j6k37tfsrtg5ikwz5ifun2rso6vpuu2w failed
[+] /lustre/home/br-kolgu/spack/opt/spack/linux-rhel8-zen3/gcc-12.2.0/openmpi-5.0.3-5pqagzyg6urjutwq4wd6xnu5lvtji4vl
[+] /lustre/home/br-kolgu/spack/opt/spack/linux-rhel8-zen3/gcc-12.2.0/fftw-3.3.10-xenz4ra6qk46p53tzriitjpoz44ax5lm
==> Error: gromacs-2024.1-qvl47qjtobwiekrtnuryfi3dug3fj7tp: Package was not installed
==> Error: Installation request failed. Refer to reported errors for failing package(s).
I don’t understand why it tries to install gcc@9.5.0
I have loaded gcc@12.2.0 and gcc@9.3.0 but it still tries to install gcc@9.5.0
Also, the oneapi compiler is present on the system so it is not spack installed
Thanks!