1

I have been happily using KVM and virt-manger on Arch Linux for about a year now. This morning, one of my VMs broke (that is another story which I don't think is related), and I decided that it would just be easiest to delete it and virt-install again.

However, after deleting this VM via the virt-manager interface, I was no longer able to start virt-manager:

$ virt-install
Traceback (most recent call last):
  File "/usr/share/virt-manager/virt-install", line 15, in <module>
    import virtinst
  File "/usr/share/virt-manager/virtinst/__init__.py", line 49, in <module>
    from virtinst.domain import *  # pylint: disable=wildcard-import
  File "/usr/share/virt-manager/virtinst/domain/__init__.py", line 5, in <module>
    from .blkiotune import DomainBlkiotune
  File "/usr/share/virt-manager/virtinst/domain/blkiotune.py", line 8, in <module>
    from ..xmlbuilder import XMLBuilder, XMLChildProperty, XMLProperty
  File "/usr/share/virt-manager/virtinst/xmlbuilder.py", line 16, in <module>
    from .xmlapi import XMLAPI
  File "/usr/share/virt-manager/virtinst/xmlapi.py", line 7, in <module>
    import libxml2
  File "<frozen importlib._bootstrap>", line 991, in _find_and_load
  File "<frozen importlib._bootstrap>", line 975, in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 671, in _load_unlocked
  File "<frozen importlib._bootstrap_external>", line 779, in exec_module
  File "<frozen importlib._bootstrap_external>", line 911, in get_code
  File "<frozen importlib._bootstrap_external>", line 580, in _compile_bytecode
EOFError: marshal data too short

It seems that libxml2 is broken in some way:

Python 3.8.3 (default, May 17 2020, 18:15:42) 
[GCC 10.1.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import libxml2
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "<frozen importlib._bootstrap>", line 991, in _find_and_load
  File "<frozen importlib._bootstrap>", line 975, in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 671, in _load_unlocked
  File "<frozen importlib._bootstrap_external>", line 779, in exec_module
  File "<frozen importlib._bootstrap_external>", line 911, in get_code
  File "<frozen importlib._bootstrap_external>", line 580, in _compile_bytecode
EOFError: marshal data too short

I have tried updating my system as well as removing and reinstalling the obvious packages, libvirt, virt-manager, libxml2 and libvirt-python, and that has not helped, nor has the somewhat dangerous pacman -Syyu.

Any ideas about what might be broken here?

I am using the LTS kernel, 5.4. Python version is 3.8. Virt-manager is 2.2.1

Also, if I just start python, I can load all the modules mentioned in the above error without any issue.

I'm close to just doing a clean reinstall, but that is a terrible bother, and I'd like to avoid it if I can just fix some dependencies in Arch

edit: As suggested in the comment, I tried running strace and here is the output (perhaps if I look at it long enough I will have some insight about which file might be corrupted). File corruption does seem likely as I ran out of disk space on root.

~]$ strace python -c 'import libxml2'
#output was too big to paste in here, so I cut out everything but the last part, which is what seemed most likely to be relevant
###..........many lines deleted....####
###..........many lines deleted....####
###..........many lines deleted....####
getcwd("/home/boss", 1024)              = 11
stat("/home/boss", {st_mode=S_IFDIR|0750, st_size=3488, ...}) = 0
stat("/home/boss", {st_mode=S_IFDIR|0750, st_size=3488, ...}) = 0
stat("/home/boss", {st_mode=S_IFDIR|0750, st_size=3488, ...}) = 0
openat(AT_FDCWD, "/home/boss", O_RDONLY|O_NONBLOCK|O_CLOEXEC|O_DIRECTORY) = 3
fstat(3, {st_mode=S_IFDIR|0750, st_size=3488, ...}) = 0
getdents64(3, /* 41 entries */, 32768)  = 1416
getdents64(3, /* 0 entries */, 32768)   = 0
close(3)                                = 0
stat("/usr/lib/python3.8", {st_mode=S_IFDIR|0755, st_size=8192, ...}) = 0
stat("/usr/lib/python3.8/lib-dynload", {st_mode=S_IFDIR|0755, st_size=8192, ...}) = 0
stat("/home/boss/.local/lib/python3.8/site-packages", {st_mode=S_IFDIR|0700, st_size=3488, ...}) = 0
stat("/usr/lib/python3.8/site-packages", {st_mode=S_IFDIR|0755, st_size=8192, ...}) = 0
stat("/usr/lib/python3.8/site-packages/libxml2.py", {st_mode=S_IFREG|0644, st_size=345896, ...}) = 0
stat("/usr/lib/python3.8/site-packages/libxml2.py", {st_mode=S_IFREG|0644, st_size=345896, ...}) = 0
openat(AT_FDCWD, "/usr/lib/python3.8/site-packages/__pycache__/libxml2.cpython-38.pyc", O_RDONLY|O_CLOEXEC) = 3
fstat(3, {st_mode=S_IFREG|0644, st_size=139264, ...}) = 0
ioctl(3, TCGETS, 0x7fffbe383200)        = -1 ENOTTY (Inappropriate ioctl for device)
lseek(3, 0, SEEK_CUR)                   = 0
lseek(3, 0, SEEK_CUR)                   = 0
fstat(3, {st_mode=S_IFREG|0644, st_size=139264, ...}) = 0
mmap(NULL, 143360, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_ANONYMOUS, -1, 0) = 0x7f2172e15000
read(3, "U\r\r\n\0\0\0\0\203\224\246^(G\5\0\343\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0"..., 139265) = 139264
read(3, "", 1)                          = 0
close(3)                                = 0
mmap(NULL, 262144, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_ANONYMOUS, -1, 0) = 0x7f2172dd5000
write(2, "Traceback (most recent call last"..., 35Traceback (most recent call last):
) = 35
write(2, "  File \"<string>\", line 1, in <m"..., 39  File "<string>", line 1, in <module>
) = 39
openat(AT_FDCWD, "<string>", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "<string>", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/usr/lib/python38.zip/<string>", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/usr/lib/python3.8/<string>", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/usr/lib/python3.8/lib-dynload/<string>", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/home/boss/.local/lib/python3.8/site-packages/<string>", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/usr/lib/python3.8/site-packages/<string>", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
write(2, "  File \"<frozen importlib._boots"..., 68  File "<frozen importlib._bootstrap>", line 991, in _find_and_load
) = 68
openat(AT_FDCWD, "<frozen importlib._bootstrap>", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "<frozen importlib._bootstrap>", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/usr/lib/python38.zip/<frozen importlib._bootstrap>", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/usr/lib/python3.8/<frozen importlib._bootstrap>", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/usr/lib/python3.8/lib-dynload/<frozen importlib._bootstrap>", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/home/boss/.local/lib/python3.8/site-packages/<frozen importlib._bootstrap>", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/usr/lib/python3.8/site-packages/<frozen importlib._bootstrap>", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
write(2, "  File \"<frozen importlib._boots"..., 77  File "<frozen importlib._bootstrap>", line 975, in _find_and_load_unlocked
) = 77
openat(AT_FDCWD, "<frozen importlib._bootstrap>", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "<frozen importlib._bootstrap>", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/usr/lib/python38.zip/<frozen importlib._bootstrap>", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/usr/lib/python3.8/<frozen importlib._bootstrap>", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/usr/lib/python3.8/lib-dynload/<frozen importlib._bootstrap>", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/home/boss/.local/lib/python3.8/site-packages/<frozen importlib._bootstrap>", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/usr/lib/python3.8/site-packages/<frozen importlib._bootstrap>", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
write(2, "  File \"<frozen importlib._boots"..., 68  File "<frozen importlib._bootstrap>", line 671, in _load_unlocked
) = 68
openat(AT_FDCWD, "<frozen importlib._bootstrap>", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "<frozen importlib._bootstrap>", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/usr/lib/python38.zip/<frozen importlib._bootstrap>", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/usr/lib/python3.8/<frozen importlib._bootstrap>", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/usr/lib/python3.8/lib-dynload/<frozen importlib._bootstrap>", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/home/boss/.local/lib/python3.8/site-packages/<frozen importlib._bootstrap>", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/usr/lib/python3.8/site-packages/<frozen importlib._bootstrap>", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
write(2, "  File \"<frozen importlib._boots"..., 74  File "<frozen importlib._bootstrap_external>", line 779, in exec_module
) = 74
openat(AT_FDCWD, "<frozen importlib._bootstrap_external>", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "<frozen importlib._bootstrap_external>", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/usr/lib/python38.zip/<frozen importlib._bootstrap_external>", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/usr/lib/python3.8/<frozen importlib._bootstrap_external>", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/usr/lib/python3.8/lib-dynload/<frozen importlib._bootstrap_external>", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/home/boss/.local/lib/python3.8/site-packages/<frozen importlib._bootstrap_external>", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/usr/lib/python3.8/site-packages/<frozen importlib._bootstrap_external>", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
write(2, "  File \"<frozen importlib._boots"..., 71  File "<frozen importlib._bootstrap_external>", line 911, in get_code
) = 71
openat(AT_FDCWD, "<frozen importlib._bootstrap_external>", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "<frozen importlib._bootstrap_external>", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/usr/lib/python38.zip/<frozen importlib._bootstrap_external>", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/usr/lib/python3.8/<frozen importlib._bootstrap_external>", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/usr/lib/python3.8/lib-dynload/<frozen importlib._bootstrap_external>", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/home/boss/.local/lib/python3.8/site-packages/<frozen importlib._bootstrap_external>", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/usr/lib/python3.8/site-packages/<frozen importlib._bootstrap_external>", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
write(2, "  File \"<frozen importlib._boots"..., 80  File "<frozen importlib._bootstrap_external>", line 580, in _compile_bytecode
) = 80
openat(AT_FDCWD, "<frozen importlib._bootstrap_external>", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "<frozen importlib._bootstrap_external>", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/usr/lib/python38.zip/<frozen importlib._bootstrap_external>", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/usr/lib/python3.8/<frozen importlib._bootstrap_external>", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/usr/lib/python3.8/lib-dynload/<frozen importlib._bootstrap_external>", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/home/boss/.local/lib/python3.8/site-packages/<frozen importlib._bootstrap_external>", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/usr/lib/python3.8/site-packages/<frozen importlib._bootstrap_external>", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
write(2, "EOFError: marshal data too short"..., 33EOFError: marshal data too short
) = 33
rt_sigaction(SIGINT, {sa_handler=SIG_DFL, sa_mask=[], sa_flags=SA_RESTORER, sa_restorer=0x7f21734763e0}, {sa_handler=0x7f21736ca3a2, sa_mask=[], sa_flags=SA_RESTORER, sa_restorer=0x7f21734763e0}, 8) = 0
munmap(0x7f2172dd5000, 262144)          = 0
munmap(0x7f2172e15000, 143360)          = 0
sigaltstack(NULL, {ss_sp=0x5610230bc580, ss_flags=0, ss_size=16384}) = 0
sigaltstack({ss_sp=NULL, ss_flags=SS_DISABLE, ss_size=0}, NULL) = 0
exit_group(1)                           = ?
+++ exited with 1 +++

edit: This thread seems promising, but I have no idea where I would check to see if __init__.py is missing.

4
  • 1
    Try strace on the python process where you import libxml2 to see what file it opens prior to marshal error. Might be a corrupt .pyc file.
    – D. SM
    Commented May 31, 2020 at 20:57
  • OK I tried that and will add it to the question (although I feel pretty clueless about interpreting it).
    – Stonecraft
    Commented May 31, 2020 at 21:28
  • 1
    Remove /usr/lib/python3.8/site-packages/__pycache__/libxml2.cpython-38.pyc, try importing again. If import succeeds, remove python-libxlml2 and reinstall.
    – D. SM
    Commented Jun 1, 2020 at 2:55
  • Yes, that worked! Put it as an answer and I'll mark it. (btw on Arch the package is just called libxml2, not python-libxml2)
    – Stonecraft
    Commented Jun 1, 2020 at 5:46

1 Answer 1

1

It is likely the reason is a corrupt .pyc file.

Try strace on the python process where you import libxml2 to see what file it opens prior to marshal error.

Then, remove that file (python does not require .pyc files to be present to work) and import libxml2 again. If the import succeeds, remove python-libxml2 and reinstall it (which should regenerate the faulty .pyc file).

3
  • Yes, that did it, thank you! Unfortunately I don't think that was all that got corrupted, as I started getting weird crashes after getting my VMs up and running.
    – Stonecraft
    Commented Jun 2, 2020 at 2:46
  • You could try force-reinstalling all installed packages.
    – D. SM
    Commented Jun 2, 2020 at 2:49
  • Too late. Arch was too high-maintenance anyway.
    – Stonecraft
    Commented Jun 3, 2020 at 6:44

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