Re: guix pull error: symlink

[Giovanni Biscuolo]

Hi Chris,

your suggestion worked, thank you!

unfortunately "guix pull" failed since it started building
gcc-cross-boot-0-5.5.0.drv and was killed by OOM

note that on subsequent test I made "guix pull --dry-run" but the pull
always triggers a build:

--8<---------------cut here---------------start------------->8---
Building from this channel:
  guix      https://git.savannah.gnu.org/git/guix.git   1e2ebf7
Computing Guix derivation for 'x86_64-linux'... /@ build-started 
/gnu/store/awmnbnb0bnwgkb3kabf05z7c11mfhxhd-gcc-cross-boot0-5.5.0.drv - 
x86_64-linux 
/var/log/guix/drvs/aw//mnbnb0bnwgkb3kabf05z7c11mfhxhd-gcc-cross-boot0-5.5.0.drv.bz2
 29475/@ build-log 29475 39
--8<---------------cut here---------------end--------------->8---

(note that meanwhile threre was a new commit in guix.git)

I'm using a QEMU VM with 1GB RAM form my testing purposes, that
configuration is definitely not suitable to build, it needs subsitutes
(using the default channel with a specific previous commit should help
me)

below the details of my test

thanks!
Giovanni

P.S.: later I realized that the swap space (2GB) on the test VM was off,
now I'm starting again with "guix pull" with swap on

Chris Marusich <address@hidden> writes:

[...]

> If so, you may be able to simply delete the following symlinks and then
> run "guix pull" again:
>
> /var/guix/profiles/per-user/gbiscuolo/current-guix-1-link
> /var/guix/profiles/per-user/gbiscuolo/current-guix-2-link
> /var/guix/profiles/per-user/gbiscuolo/current-guix-3-link
> ...
> /var/guix/profiles/per-user/gbiscuolo/current
>
> Of course, before deleting anything, please be sure to record each of
> the symlinks, their permissions, and their targets so that you can undo
> the deletion if necessary.  Please be careful when deleting.
>
> If all goes well, when you run "guix pull", Guix should automatically
> migrate your profile generations successfully into the
> /var/guix/profiles/per-user/gbiscuolo directory.  After that, you won't
> have to worry about it again (for the gbiscuolo user, at least).

oh yes, your suggestion worked: "git pull" started upgrading again

unfortunately it also started building derivations (sorry I do not have
a list), e.g.:

--8<---------------cut here---------------start------------->8---
Updating channel 'guix' from Git repository at 
'https://git.savannah.gnu.org/git/guix.git'...
Building from this channel:
  guix      https://git.savannah.gnu.org/git/guix.git   6845fdc
building 
/gnu/store/awmnbnb0bnwgkb3kabf05z7c11mfhxhd-gcc-cross-boot0-5.5.0.drv...
[...]
gcc-5.5.0/zlib/zutil.c
gcc-5.5.0/zlib/zutil.h
phase `unpack' succeeded after 1180.6 seconds
starting phase `unpack-gmp&co'
gmp-6.0.0/
gmp-6.0.0/.gdbinit
gmp-6.0.0/AUTHORS
gmp-6.0.0/COPYING
[...]
--8<---------------cut here---------------end--------------->8---

finally failing for OOM

--8<---------------cut here---------------start------------->8---
build/genautomata ../../gcc-5.5.0/gcc/common.md 
../../gcc-5.5.0/gcc/config/i386/i386.md \
  insn-conditions.md > tmp-automata.c
make[2]: *** [Makefile:2156: s-attrtab] Killed
make[2]: *** Waiting for unfinished jobs....
/gnu/store/8z9avbgm73nzrbkhscps68gcpfipgllc-bootstrap-binaries-0/bin/bash 
../../gcc-5.5.0/gcc/../move-if-change tmp-automata.c insn-automata.c
echo timestamp > s-automata
make[2]: Leaving directory 
'/tmp/guix-build-gcc-cross-boot0-5.5.0.drv-0/build/gcc'
make[1]: *** [Makefile:4105: all-gcc] Error 2
make[1]: Leaving directory '/tmp/guix-build-gcc-cross-boot0-5.5.0.drv-0/build'
make: *** [Makefile:859: all] Error 2
Backtrace:
In ice-9/boot-9.scm:
 157: 12 [catch #t #<catch-closure c92c80> ...]
In unknown file:
   ?: 11 [apply-smob/1 #<catch-closure c92c80>]
In ice-9/boot-9.scm:
  63: 10 [call-with-prompt prompt0 ...]
In ice-9/eval.scm:
 432: 9 [eval # #]
In ice-9/boot-9.scm:
2320: 8 [save-module-excursion #<procedure cc0b80 at ice-9/boot-9.scm:3961:3 
()>]
3966: 7 [#<procedure cc0b80 at ice-9/boot-9.scm:3961:3 ()>]
1645: 6 [%start-stack load-stack #<procedure cc1dc0 at ice-9/boot-9.scm:3957:10 
()>]
1650: 5 [#<procedure cc2060 ()>]
In unknown file:
   ?: 4 [primitive-load 
"/gnu/store/1ybknnj20hqz1mnzi3my0hpd3mj7gpjz-gcc-cross-boot0-5.5.0-guile-builder"]
In ice-9/eval.scm:
 387: 3 [eval # ()]
In srfi/srfi-1.scm:
 830: 2 [every1 #<procedure e62a00 at 
/gnu/store/lpals6qq7ccbdldzamis7x9mv2p7g4sb-module-import/guix/build/gnu-build-system.scm:795:9
 (expr)> ...]
In 
/gnu/store/lpals6qq7ccbdldzamis7x9mv2p7g4sb-module-import/guix/build/gnu-build-system.scm:
 799: 1 [#<procedure e62a00 at 
/gnu/store/lpals6qq7ccbdldzamis7x9mv2p7g4sb-module-import/guix/build/gnu-build-system.scm:795:9
 (expr)> #]
In 
/gnu/store/lpals6qq7ccbdldzamis7x9mv2p7g4sb-module-import/guix/build/utils.scm:
 616: 0 [invoke "make" "-j" ...]

/gnu/store/lpals6qq7ccbdldzamis7x9mv2p7g4sb-module-import/guix/build/utils.scm:616:6:
 In procedure invoke:
/gnu/store/lpals6qq7ccbdldzamis7x9mv2p7g4sb-module-import/guix/build/utils.scm:616:6:
 Throw to key `srfi-34' with args `(#<condition &invoke-error [program: "make" 
arguments: ("-j" "2" 
"LDFLAGS=-Wl,-rpath=/gnu/store/8zqhf670igizfl895hnhhmx9vz6zyzsj-glibc-bootstrap-0/lib
 -Wl,-dynamic-linker 
-Wl,/gnu/store/8zqhf670igizfl895hnhhmx9vz6zyzsj-glibc-bootstrap-0/lib/ld-linux-x86-64.so.2"
 "BOOT_CFLAGS=-O2 -g0") exit-status: 2 term-signal: #f stop-signal: #f] 
3e46180>)'.
builder for 
`/gnu/store/awmnbnb0bnwgkb3kabf05z7c11mfhxhd-gcc-cross-boot0-5.5.0.drv' failed 
with exit code 1
build of /gnu/store/awmnbnb0bnwgkb3kabf05z7c11mfhxhd-gcc-cross-boot0-5.5.0.drv 
failed
View build log at 
'/var/log/guix/drvs/aw/mnbnb0bnwgkb3kabf05z7c11mfhxhd-gcc-cross-boot0-5.5.0.drv.bz2'.
cannot build derivation 
`/gnu/store/qhwr5smc6nsr0j8nh3hfa0h73xydc9ck-gcc-cross-boot0-wrapped-5.5.0.drv':
 1 dependencies couldn't be built
cannot build derivation 
`/gnu/store/1wp0jy2sdxgyn0mxvds75jan2c0az0q0-glibc-2.28.drv': 1 dependencies 
couldn't be built
building /gnu/store/8qsid2pqlav3454pzw783j6zy2n0j2l6-perl-boot0-5.28.0.drv...
cannot build derivation 
`/gnu/store/cz4sr5whzf3qhp8c47bzlfzcxxwl485i-python2-2.7.15.drv': 1 
dependencies couldn't be built
guix pull: error: build failed: build of 
`/gnu/store/cz4sr5whzf3qhp8c47bzlfzcxxwl485i-python2-2.7.15.drv' failed
--8<---------------cut here---------------end--------------->8---

OOM from dmesg:

--8<---------------cut here---------------start------------->8---
[263725.076217] genautomata invoked oom-killer: 
gfp_mask=0x6280ca(GFP_HIGHUSER_MOVABLE|__GFP_ZERO), nodemask=(null), order=0, 
oom_score_adj=0
[263725.232974] genautomata cpuset=/ mems_allowed=0
[263725.234315] CPU: 1 PID: 29391 Comm: genautomata Not tainted 4.19.8-gnu #1
[263725.235668] Hardware name: QEMU Standard PC (i440FX + PIIX, 1996), BIOS 
1.10.2-1 04/01/2014
[263725.237169] Call Trace:
[263725.238684]  dump_stack+0x63/0x85
[263725.240130]  dump_header+0x6e/0x295
[263725.241559]  oom_kill_process+0x25d/0x280
[263725.243365]  out_of_memory+0x2af/0x4d0
[263725.244842]  __alloc_pages_slowpath+0xa6a/0xdf0
[263725.246305]  __alloc_pages_nodemask+0x298/0x2c0
[263725.248053]  alloc_pages_vma+0x88/0x1f0
[263725.249539]  __handle_mm_fault+0x8b8/0x12b0
[263725.250986]  handle_mm_fault+0xe3/0x220
[263725.252468]  __do_page_fault+0x250/0x4d0
[263725.253923]  do_page_fault+0x2d/0xf0
[263725.255372]  ? async_page_fault+0x8/0x30
[263725.256947]  do_async_page_fault+0x51/0x80
[263725.258413]  async_page_fault+0x1e/0x30
[263725.259878] RIP: 0033:0x7ffff77b1257
[263725.261367] Code: Bad RIP value.
[263725.262852] RSP: 002b:00007fffffffb500 EFLAGS: 00010206
[263725.264605] RAX: 0000000000000261 RBX: 00007ffff0000020 RCX: 
0000000000000004
[263725.266123] RDX: 00007ffff00afdb0 RSI: 00007ffff00b0da0 RDI: 
00007ffff00b0000
[263725.267639] RBP: 0000000000000ff5 R08: 0000000000000000 R09: 
00000000000b0000
[263725.269229] R10: 0000000000000250 R11: 0000000000000206 R12: 
0000000000000fe0
[263725.270877] R13: 00007ffff00afdc0 R14: 00007ffff0000078 R15: 
00007ffff00afdb0
[263725.272538] Mem-Info:
[263725.274199] active_anon:234404 inactive_anon:0 isolated_anon:0
                 active_file:9 inactive_file:28 isolated_file:0
                 unevictable:4 dirty:0 writeback:0 unstable:0
                 slab_reclaimable:3540 slab_unreclaimable:4393
                 mapped:2 shmem:0 pagetables:865 bounce:0
                 free:5708 free_pcp:67 free_cma:0
[263725.283600] Node 0 active_anon:937616kB inactive_anon:0kB active_file:36kB 
inactive_file:112kB unevictable:16kB isolated(anon):0kB isolated(file):0kB 
mapped:8kB dirty:0kB writeback:0kB shmem:0kB shmem_thp: 0kB shmem_pmdmapped: 
0kB anon_thp: 163840kB writeback_tmp:0kB unstable:0kB all_unreclaimable? yes
[263725.288764] Node 0 DMA32 free:22832kB min:22528kB low:28160kB high:33792kB 
active_anon:937616kB inactive_anon:0kB active_file:116kB inactive_file:200kB 
unevictable:16kB writepending:0kB present:1048056kB managed:1010468kB 
mlocked:16kB kernel_stack:1952kB pagetables:3460kB bounce:0kB free_pcp:268kB 
local_pcp:188kB free_cma:0kB
[263725.294467] lowmem_reserve[]: 0 0 0 0
[263725.296640] Node 0 DMA32: 370*4kB (UME) 287*8kB (UEH) 261*16kB (UMEH) 
119*32kB (UMEH) 73*64kB (MEH) 22*128kB (ME) 8*256kB (MEH) 1*512kB (H) 1*1024kB 
(H) 0*2048kB 0*4096kB = 22832kB
[263725.300795] Node 0 hugepages_total=0 hugepages_free=0 hugepages_surp=0 
hugepages_size=2048kB
[263725.302843] 53 total pagecache pages
[263725.305140] 0 pages in swap cache
[263725.307263] Swap cache stats: add 0, delete 0, find 0/0
[263725.309295] Free swap  = 0kB
[263725.311150] Total swap = 0kB
[263725.313094] 262014 pages RAM
[263725.314903] 0 pages HighMem/MovableOnly
[263725.316780] 9397 pages reserved
[263725.318546] 0 pages cma reserved
[263725.320431] 0 pages hwpoisoned
[263725.322295] Tasks state (memory values in pages):
[263725.324261] [  pid  ]   uid  tgid total_vm      rss pgtables_bytes swapents 
oom_score_adj name
[263725.326090] [    166]     0   166     1191      360    49152        0       
      0 udevd
[263725.327924] [    220]     0   220   135344       67   106496        0       
      0 nscd
[263725.329888] [    228]     0   228     3009      132    61440        0       
      0 guix-daemon
[263725.331747] [    231]     0   231      717       62    40960        0       
      0 syslogd
[263725.333713] [    232]     0   232      591       12    40960        0       
      0 mingetty
[263725.335586] [    233]     0   233      591       12    40960        0       
      0 mingetty
[263725.337535] [    234]     0   234      591       13    45056        0       
      0 mingetty
[263725.339370] [    235]     0   235      591       12    40960        0       
      0 mingetty
[263725.341293] [    236]     0   236      591       13    49152        0       
      0 mingetty
[263725.343096] [    252]     0   252     1556      287    49152        0       
      0 dhclient
[263725.344999] [    264]     0   264      745       54    45056        0       
      0 login
[263725.346824] [    265]  1000   265     2122      460    53248        0       
      0 bash
[263725.348736] [   1177]     0  1177     1960      135    57344        0       
  -1000 sshd
[263725.350537] [   1178]     0  1178     1998      147    61440        0       
      0 sshd
[263725.352427] [   1180]  1000  1180     2032      161    61440        0       
      0 sshd
[263725.354194] [   1181]  1000  1181     2106      438    57344        0       
      0 bash
[263725.355944] [   1182]  1000  1182     1653       89    49152        0       
      0 screen
[263725.357850] [   1183]  1000  1183     1719      165    49152        0       
      0 screen
[263725.359593] [   1184]  1000  1184     2172      516    57344        0       
      0 bash
[263725.361426] [   1318]     0  1318     1764      117    53248        0       
      0 sudo
[263725.363139] [   1319]     0  1319     1507       95    49152        0       
      0 su
[263725.364933] [   1320]     0  1320     2128      462    57344        0       
      0 bash
[263725.366619] [   1388]  1000  1388     2120      444    49152        0       
      0 bash
[263725.368394] [   1389]     0  1389     1764      116    53248        0       
      0 sudo
[263725.370061] [   1390]     0  1390     1507       96    49152        0       
      0 su
[263725.371712] [   1391]     0  1391     2324      653    53248        0       
      0 bash
[263725.373425] [   1422]  1000  1422     2146      486    57344        0       
      0 bash
[263725.374971] [  16084]     0 16084     1998      147    53248        0       
      0 sshd
[263725.376563] [  16086]  1000 16086     2028      161    53248        0       
      0 sshd
[263725.377986] [  16087]  1000 16087     1894      235    49152        0       
      0 sh
[263725.379345] [  16210]  1000 16210    88537    36125   589824        0       
      0 .guix-real
[263725.380765] [  16223]     0 16223     5627     2518    77824        0       
      0 guix-daemon
[263725.382061] [  16225]     0 16225    34080     3805   151552        0       
      0 guix substitute
[263725.383302] [  16229]     0 16229    17328     2969   139264        0       
      0 guix offload
[263725.384592] [  16234] 30001 16234    34623    11738   163840        0       
      0 .guile-real
[263725.385753] [  17821] 30001 17821     1983      396    45056        0       
      0 make
[263725.386881] [  17823] 30001 17823      431       51    32768        0       
      0 bash
[263725.388080] [  17836] 30001 17836     2017      450    45056        0       
      0 make
[263725.389231] [  26453] 30001 26453      466       71    32768        0       
      0 bash
[263725.390339] [  26461] 30001 26461      466       83    32768        0       
      0 bash
[263725.391445] [  26484] 30001 26484     4074     2448    61440        0       
      0 make
[263725.392666] [  29382] 30001 29382   134420   117369   983040        0       
      0 genattrtab
[263725.393797] [  29390] 30001 29390      431       22    32768        0       
      0 bash
[263725.394925] [  29391] 30001 29391    63890    45834   409600        0       
      0 genautomata
[263725.396159] Out of memory: Kill process 29382 (genattrtab) score 465 or 
sacrifice child
[263725.397352] Killed process 29382 (genattrtab) total-vm:537680kB, 
anon-rss:469476kB, file-rss:0kB, shmem-rss:0kB
[263725.509294] oom_reaper: reaped process 29382 (genattrtab), now 
anon-rss:0kB, file-rss:0kB, shmem-rss:0kB
--8<---------------cut here---------------end--------------->8---

>> [1] maybe I mede some error using "sudo guix..." instead of the recommended 
>> "sudo -E guix..."
>
> That could be.  Hopefully my suggestion will help!
>
> -- 
> Chris

-- 
Giovanni Biscuolo

Xelera IT Infrastructures

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